Metroid/WMG

Tags have been added but watch out for spoilers.

Sylux is a flash-clone of Samus.

 * The Galactic Federation has always desired to have their own personal Hunter directly under their control. Though Samus operates fairly consistently for the Feds, the brass has always felt uncomfortable with the possibility of her learning too much (Which pretty much happened during the events of Fusion). Before Zero Mission, the Feds secretly begin working on a supersoldier program, codenamed SYLUX. The first was a flash-clone of Samus, less of a prototype, more of proof-of-concept. Sylux to begin with is very emotionally unstable, having been forced to reach full maturity within a few years and being treated as nothing other than a weapon. Eventually, when they were to terminate the original and begin full-scale production, Sylux became consumed with rage and devastated the entire facility stealing the prototype suit and gunship in the process. The project was covered up and never heard about again. The Feds, now knowing what kind of power they were dealing with decided to move on and attempt to capture and control Dark Samus, and failing that moved on to the SA-X.

Sylux is Samus from the future.

 * Samus after what happened on the Bottleship, and BSL, is being hunted by the GF. Unfortuantly  has limited functionality due to a fail-safe built into the ship by the  . It is revealed that the entire reason why they allowed her to go to   in the first place was because of the ship being modified not only to allow near-total remote control of the entire station, but also the inclusion of multiple fail-safes, including a self-destruct. The   want to capture samus to make use of her battle armour and so do not activate the self-destruct, instead setting it to activate should the ship not recive a code from them every day, this prevents Samus from escaping GF space. In an incident involving a wormhole, Samus' ship and several GF fighters she is sent back in time, due to not recieving the code not to self destruct (the code was not broadcast as it was before it was even created), Samus' ship will blows up in one day,  warns her about the self-destruct, and gets really pissed off at the GF due to this being, effectively, the second time he would be killed because of the  . Realising she needs to find a way to stop the   and get a new suit (her fusion suit being made of the organic components of her chozo suit begins to have issues due to the massive amount of DNA modification induced by the  ) she spends this day getting Adam to hack into   databases, getting her access into one of the   black-op projects, specifically an attempt to create battle armour like Samus' the name of the project prototype is "Sylux" and has the ID 024-105 as when compared to "Samus" using an a-z alphabet with the letter after z being a, forming a cycle, the minimum difference between each letter is 02105, as in the year 2105, when the project began, (GF was founded in 2000, so it's a reasonable time period for the game) additionally "sylux" minus "samus" is 024-105 (the '-' is formed by '-1', hence the ID). Just before her ship blows up samus manages to copy some of Adam's Program to an external storage device and escape. She then proceeds to use the access gained by Adam's hacking to enter the research facility where "Sylux" is and steals it along with the 'Delano 7' in which she installs the partially copied version of Adam (though as it is only a partial copy it's effectively insane). After sometime she recieves the message from   that starts Metroid Prime: Hunters and heads there in the hopes of warning herself about the   however upon finding herself her past self open fires assuming her to be another hunter searching for the Octoliths she is forced to fight back calling the 'Delano 7' to escape, Adam being crazy attack's samus' past self stopping only in brief moment of lucidity caused by being repeatedly shot in the face  appendage turret, and eventually escapes and for the rest of the game spends all her time trying to tell herself about  . After Hunters she continues looking for herself, due to having had to escape the   she lost herself (this confusing anyone yet). In this time she upgrades the 'Delano 7' to the 'Delano 9' (hmmm... 7, they really like 7... mabye there's a connec... back to the WMG) using surving parts from her old ship and at the end of   well you know the rest.

Ridley is the reincarnation of Samus' father.

 * Ridley was the father of Samus and he was abusive, alcholic, and violent. When Samus could stand it no longer she killed him, but Ridley was a satanist so he was reborn as the immortal Baal. That, or he's a very popular character who can't be killed off.
 * It's established cannon that a) Samus cared quite deeply for her parents, b) She was orphaned at a young age and raised by the Chozo and c) It was Ridley who orphaned her (although the later was only in the metroid manga and might not be cannon).
 * Word of God is that the manga is canon.
 * Those were really Samus's adopted parents and she suppressed the memory of killing her father. Alternatively her mom killed him and Samus was too young to remember or Ridley is too popular not to come back.

Adam!Computer genuinely did believe that Adam's sacrifice was foolish.
"Adam: Did this "Adam" care for you? Would he sit in a safe Command Room and order you to die? Samus: He would understand that some must live and some must die... He knew what it meant. He made that sacrifice once. Adam: So he chose life for you? Our fair warrior, Samus Aran... Your Adam gave his life so that you might keep yours... For the sake of the universe... Samus: ......... Adam: How foolish. Samus: How dare you! How could you hope to understand, machine?"
 * When Samus let slips Adam's name to the computer, the following exchange takes place.


 * It seems a little harsh when you consider Adam's actual fate, but

Nintendo will never continue the series chronologically after Fusion.

 * It's kinda painful how much they have been adamantly avoiding doing this, or just plain trying to forget about it. Fusion was made several years ago, yet lets think of all the things that have been released since then. All three Prime Games, Hunters, Zero Mission, hell, even Other M seems to be set before it. It almost seems like Nintendo has considers Samus Ruined FOREVER now that she has Metroid DNA in her, or something... or maybe its because she spoke in Fusion? The outlaw angle is too difficult to pull off? It just seems like Nintendo REALLY doesn't want to continue Samus' story past Fusion, which is a pity, given that her physical appearance in the 100% ending of Fusion is the best of the series, by and far better than her outfit in Zero Mission, both the Zero Suit and her red tank top + shorts.
 * Alternatively, it could be for the same reason Camelot took so long to make Golden Sun 3: they don't want to half-ass it, and are waiting to come up with a worthy idea. Also it was said in interview that the creator wanted to tie Super Metroid to Fusion before going to the latter sequel. Implying that the next one after Other M would be set after Fusion.
 * It should be considered, however, that, with exception of Other M, all Metroid games after Fusion where either a remake or made by a third party, being more like spin-offs.
 * Personally, I think it has something to do with the fact that Fusion messed with Clothes Make the Legend. Better to continue hyping stuff with the orange Power Suit rather than spend resources making the blue Fusion Suit that iconic. (Yes, I know the Fusion Suit turned orange at the end. It's still very different from the Power Suit, and we all know Samus would lose her upgrades anyway.)
 * You don't see it, do you. Nintendo will of course have Samus go on another sprawling adventure in which she exorcises the Metroid DNA and regains her suit. Problem solved. Somehow.
 * And, naturally, the act of doing so will produce a Fusion-suited evil mostly-metroid clone Samus that will be the Big Bad of that game.
 * I always thought it had something to do with the fact that the Metroids are now extinct and to continue the series after its namesakes are gone would be pointless.
 * All gone... except for Samus herself, who has Metroid DNA in that game. Presumably, this means that they can be cloned from her blood, which would be an excellent story-driving plot point.
 * Which is, in fact, the DNA of a Queen metroid.
 * Hmm, Metroid: Resurrection sounds like it would be a good game!
 * It doesn't seem all that strange that chronologically the series would end there. Samus fought the Space Pirates and the metroids for a long time until finally eliminating the threat of both. There was a lot going on between chapters of that central conflict, but eventually that's where it ended. The metroid extermination prompted the explosion of the X-parasite population, which began to take over everything, ever. If left unchecked there's no telling what they would have done. Samus fought one last time and this time may have destroyed the biggest enemy of them all and saved countless civilizations. The greatest threats to the safety of all have been taken out, and Samus rides off into the sunset. Not only that, but she rides off reunited with her animal friends, with Adam, and carrying the baby metroid with her in body and spirit. Can you think of a better ending? I can't. At least not with Chozodia in ruins and its people apparently lost forever. All that's left to do now is delve deeper into the story that's already been told.
 * Um, except that Samus just found out that the Federation has been confirmed to be dipping into highly dangerous and probably illegal research with extremely dangerous parasites ALA the Space Pirate Command and Samus has just blown up one research station and lived to tell the tale. If they had one uber-secret research facility for studying the X and Metroids, they can have many more. And regardless, it is all too probable that whoever was running the show there has come to the conclusion that She Knows Too Much. To just act like that is the end of the story, completely happy ending game over is more than a little bit of a wallbanger.
 * Then again, the genuine-article final game of the series wouldn't suit the theme of the series very well if it tried to pull a Happily Ever After.
 * Part of the problem may be that a game where you are evading pursuit of overwhelming hostile forces (one imagines the Federation would have more and better-organized assets -- and firepower! -- than the Space Pirates by a long shot) would be hard to reconcile with the slow-paced, exploratory gameplay of the series thus far, which usually involves Samus delving deeply into whatever mystery is afoot. It could be done, but future games would almost certainly have to treat such pursuit as a background element. Confronting the implications of such a plotline directly would probably necessitate a new style of gameplay, which would surely inspire a tremendous outcry from the existing fanbase.
 * Nintendo already took its sweet time to release a new Metroid game that lived up to the original, (and Fusion) it's not like we should be expecting a sequel the next year. You think Valve is bad, but Nintendo always takes ages to release games and they're almost always worth every minute.
 * It is very likely that Fusion was meant to be the last chronologically. If you take three things into consideration you can see why this is. 1) The X are still out there, just stranded in space. The X have only been shown to be defeated by having their 'life energy' drained. The Metroid were created specifically to do this, and by having Metroid DNA Samus is able to also. So, not only is there no evidence that the explosion of the BSL destroyed the X, but there is evidence that it definently did not. This means that the X are just stranded in space instead of completely eliminated. 2) Samus is a wanted terrorist. Even though the destruction of the BSL and SR 388 was necessary, Samus still destroyed a research facility and a large habitat of creatures. That is today's equivalent of destroying a large science lab and a wilderness preserve. Samus would be considered to be a terrorist. 3) The GF will send a large amount of vessels to the destroyed location of the BSL and SR 388. Not only will the GF be trying to track down Samus, they will also want to record and investigate what happened at the site. So, the X are waiting for something to come by that they can use to spread, and we know that the GF will come by that way. We also know that they X can go through walls, so they can get in the vessels. So we know that the X threat is not over, we also know that the only thing that can stop the X, Samus, will be on the run from the GF. By the time that the GF realize that Samus was correct in what she did, it will be too late, and the X will already be too far widespread to defeat. the Metroid Series has a serious Downer Ending.
 * Fan theories. It is stated in Fusion that when explosions get big enough X can be killed by them. The X are dead until canon says otherwise.

Ridley has a healing factor.
While it is established that the Space Pirates have cloning technology, it alone cannot explain why Samus fought Ridley six times over the course of the series, while Mother Brain and Kraid only got two battles. In addition, she fought him twice during Metroid Prime 3, in deadly skirmishes that took place a mere month apart. And, after his body was blasted in two and the planet Zebes (the sole remaining Space Pirate base of operations) was blown to smithereens at the end of Super Metroid, he was still able to be captured by the Federation in Metroid Fusion! The only way this makes any sense is if he can recover from a fatal injury without the need for cloning. While the Space Pirates fooled around with his body for purposes of adding mechanical attachments, he didn't need them to live. Also, if he was cloned at any point in the series, it was between Corruption and Super Metroid, largely due to the nature of being a Leviathan guardian and the subsequent destruction of Phazon in its entirety.
 * Confirmed here with a twist....
 * Big deal, I do that every day.
 * Assuming the manga is even canon. Besides     . It's likely that he's revived via a combination of cloning and Brain Uploading.
 * Word of God stated the manga is canon, as noted above. So confirmed, Ridley does have a healing factor.
 * This may explain why you find him in a freezer in Fusion. Cold may slow down or stop his healing factor.

Metroids drain electrical charge from their prey.
In Metroid Prime it's said by Space Pirate researchers that those drained by metroids don't lose fluids or any other material; in Super Metroid we see enemies drained by the giant metroid remain intact, but end up desiccated and crumble easily. If metroids drain electrical charge then the electrons of atoms slip down into lower orbitals as their energy is taken. This causes molecular bonds-mostly covalent to weaken because electrons are no longer being shared. Desiccation is a side effect from the water molecules separating into hydrogen and oxygen atoms-which promptly evaporate.
 * One theory is that Metroids drain the prey's soul. Or separate their soul from the bodies (seeing that they were created by a technically pacifist and very spiritual race, making them kill the target's soul might seem a bit exessive)
 * Also makes sense given that metroids seem to preferentially latch onto their victims' heads when feeding. Presumably they're tapping the electrical output generated by the victim's brain. That means they're capable of feeding from inorganic sources, such as the Power Suit's shielding system, but they don't like doing it (a scan in the Phazon Mines of Metroid Prime revealed this - they don't do well in captivity unless they're fed live prey, and straight electricity actually makes them sick).
 * Alternately, they can absorb any form of energy (including electricity) but prefer to feed off life force (especially that of the X parasite). Perhaps the ability to drain life force was the only sure-fire way for a Metroid to deal with any X-parasite that would try to infect it (the little buggers are microscopic, after all). This could also explain why they're so vulnerable to cold, as well, since cold isn't a type of energy; it's a lack of thermal energy.
 * But the problem being (which is what I assume led to this very WMG) WHAT THE HELL IS LIFE FORCE?
 * Not a problem, life force is something that exists in the setting that less advanced civilizations like the Federation and Space Pirates don't fully understand, as evident by the scans of ghosts, Gorea and Metroid feeding.

Ridley & Kraid are somehow related to the Chozo.
Think about it: both of them look like dinosaurs to some degree & the Chozo are birds which evolved from dinosaurs. Perhaps they're Chozo who were born with some kind of extreme atavistic disorder that caused them to be shunned from society & turned them into the vicious warlords we all know & love. Maybe it was intentional & they're the results of biological experiments to create a super soldier by unlocking genes left over from their primitive ancestors. We know that inspite of their peace-loving appearance, the Chozo dabbled in some pretty nasty stuff with the Metroids & even created Mother Brain, so it's not so far fetched. Or perhaps they're the last survivors of an ancestor species out for revenge for driving them to extinction.
 * I remember reading that Kraid is actually from a planet like earth but where the dinosaurs didn't die off and after a civil war became the leader of the planet and that Ridley is the last of a species of dragon like creatures native to Zebes.
 * Ridley being a creature native to Zebes is mentioned in the manul of the first game, but later background seems to contradict this, as Ridley was the leader of the Space Pirates before they conquered Zebes. Orfcourse he could be a member of a species that lived on the planet before the Chozo came and was driven off by them. That would make him very old (potentially several thousand years old), but then again, dragons are known for their long lifespan. In the manga it's implied that the Chozos have atleast had some contact with his species at some point.
 * Problem here is saying the Chozo are birds. They resemble birds. They are nothing like any Earth-based creature. And it is also unwise to assume that evolution on any other planet would even remotely resemble that of our fossil record, so the fact that they "look like dinosaurs, and birds evolved from dinosaurs" probably has no bearing in any other place in the universe. Except Star Trek: Voyager.

Sylux will be the Big Bad of the next Metroid game.
In Metroid Prime: Hunters, a lot more detail is given to Sylux than the other hunters. Sylux gets a Cool Ship, more scan info, and Sylux's backstory goes on to establish this particular hunter as having a specific beef with Samus. While this could also be true of the Space Pirate hunter, he doesn't get said Cool Ship or the same sort of "puzzle fight" Sylux gets. Also, in interviews, the developers specifically said they wanted to do more games with the Hunters. While they did use Noxus' race again in Metroid Prime 3, it doesn't seem unlikely to me that they could use Sylux as their next Big Bad--given that it's been established that the Federation wants Sylux gone too. Also, since all the other potential bad guys are Deader Than Dead, it seems like the best option. Well, better than making ANOTHER Samus clone, anyway. Which leads to my next theory...
 * Weavel's ship is seen when you board the last level, and he actually has more to work with with his given backstory. No puzzle fight because he was early in the game.
 * This seems very likely seeing that

Sylux is a girl.
I realized as I was reading up information about the game (and the in-game info as well) that both go out of their way to avoid pronouns when talking about Sylux. Sylux is almost always refered to as just "Sylux," and I do believe the one time they had to stoop to pronouns, they just went with "it." While it's true that Sylux's identity is supposed to be secret, it would be a massive WTF moment if the Metroid series managed to pull off its own favorite trope not once but twice. Since nobody would be expecting it AGAIN, it'd be even more surprising--or something. To make matters even weirder, perhaps Sylux is another refugee of the attack on the colony Samus came from, only adopted by the Space Pirates instead or somesuch. (No, I can't figure out why they'd do that. Maybe to experiment on her.) Also, if Sylux were to be the Big Bad, it would be almost contractually required for her to be female--the Big Bad in every Metroid game is almost always female in some fashion. (The first Metroid and Super Metroid had Mother Brain, though to be fair she could be genderless. Metroid II had the Queen Metroid. All the Prime games except Hunters had Dark Samus, though she's still in her naescent form in the first--she and the SA-X from Metroid Fusion are both Samus clones, so of course they're female.) Yeah, OK, so it's a bit of a kludge, but it's the best I got.
 * The last boss of Fusion was the Omega Metroid (gender unspecified) and and the last boss of Zero Mission was the robotic Ridley (genderless, but based on a male creature). Other thna that, this theory seems quite likely.
 * While reading this, I got a mental image of a girl in Sylux's armor sans helmet, similar to Samus, but with black hair and a nasty scowl. That would be awesome.
 * Furthermore in Super Smash Bros Brawl, Sylux's throphy entry avoids using gender-specific pronouns, calling Sylux "it" instead of him or her. Every other hunter, even the very nonhuman ones are referred by gender-specfic pronouns.
 * Do we know that Samus is an only child?
 * If you go by the manga, then yes, she is.
 * Further proof? Look at this picture of Sylux. It's downright wasp-waisted, and it has Hartman Hips. Hmmm.... Also, the Metroid Wikia seems to have this same theory.
 * Addition to th theory: Sylux is a very short human female. to get that waist with those legs, Sylux would have to have removed half of hir internal organs. If she is just very short, especially considering that Samus is 6'1", she could be in a very small Giant Mech instead of a powersuit, with her arms and head inside the chest of the suit and her legs only in the suit's "thighs". This also reasons why the head is so small: it's just a closed-circuit camera.
 * Now, the proportions of the Metroid universe aren't very good indicators. Compare Samus' shoulders in and out of her suit. While only wearing a jumpsuit, her shoulders look fine. But inside the suit, they appear to become several inches wider, judging from the arm placement. Also, look at the Fusion suit.
 * A girl, maybe, but not a human girl. Unless the federation added a scfi movie monster synthesizer into their suit for no good reason, then human beings typically don't make those kind of sounds...then again the Metal Gear roars for no good reason...
 * Intimidation value?

Ridley and Kraid are the names of their respective species
That's basically it. It explains the Ridley thing better than him having a healing factor, and it fits with what we know about the way pirate society works. This also means that at any one time, there are multiple Ridleys. which begs the question, why not just clone an army of Kraids or Ridleys or even both? Simple; cloning takes resources, and Ridley is too big a clone for it to be cost effective for there to be more than one or two of him at the same time. Doubly so for Kraid, and eventually they just stopped because Ridley was more useful.
 * Also explains how some Ridleys remain fully organic, while others receive cybernetic augmentations.
 * This is just because the games are not released sequentially. It goes Metroid(Zero Mission), Prime, Hunters, Prime 2, 3, Metroid II, Super Metroid, Other M, and finally Fusion. So he's organic, then gets upgraded, then gets Killed Off for Real, then returns, gets killed again, get X'ed.
 * Actually, I just realized what's wrong with that: He's organic in Super, which is after Meta, but before the Killed Off for Real part.
 * Not a bad theory, except the scan data for Ridley seems to suggest otherwise.

Ridley is a Pokémon
Which is why he always comes back. Regardless of how much, or what kind of damage you do to him, he's just fainted. Blown to bits by missiles? Fainted. Stuck in a planetary cancer when it collapsed? Fainted. Infected and eaten by X Parasites? Fainted. It doesn't matter what happened, a quick trip to a Pokemon Center and he's right as rain.
 * Meta Ridley in Prime was the result of holding some Space Pirate weapons. Omega Ridley was a forced evolution that was reversed when all the Phazon was destroyed.
 * Something in Other M supports this idea.

Ridley isn't cloned, or immortal. He's just really lucky/smart.
While it's obvious Ridley has a high degree of durability and regenerative capabilities, his multiple appearances are the result of mostly luck, and one ingenious plan. Ridley's reappearance in every game has been accounted for, save moving from Metroid Prime 3 into Super Metroid. Metroid to Metroid Prime, his remains are recovered and he's repaired. Same with Metroid Prime to Metroid Prime 3. True, both defeats left him almost utterly obliterated, but it's clear that the provided explanation is supposed to be sufficient. But at the end of Prime 3, he's literally vaporized. How could he return?

So here's what I think happened: Ridley, being the only other Leviathan guardian with sentience (he's also said to be incredibly intelligent) did the exact same thing Metroid Prime did: use Phazon to reconstitute a body. The difference here being that he always planned to do this.

Dark Samus takes over the Colossus, takes it to Phaaze, and then invades the Pirate Homeworld, where Ridley is chillaxin'. He smells an opportunity to restore himself to full combat potential, and so agrees, willingly, to follow Dark Samus (note that he has none of the telltale signs of corruptions all the other Pirates do, such as emaciated forms and Phazon deposits on their flesh). Later, at the invasion on Norion, he puts up a token fight with Samus for good show, and then allows her to escape (this makes more sense than him not turning around and flying back up the shaft). He returns to the Pirate Homeworld, and merges himself with the Phazon there, anticipating two things: that Samus will come and murder him, and that she will then go on to murder Phaaze. In the interim, he can construct a new body, made entirely of Phazon, and when it's all rendered inert, all that would be left would be his original, organic body. He cannot simply kill himself, though, because Dark Samus will sense his motives and murder him as a challenge to her authority. And the reason the fight with him is so intense if he wants you to kill him? He didn't anticipate just how strong the will of Phazon was, and was briefly lost to it, but regained control after his corporeal death.

With his organic body, he regroups the Pirates, relocates them to a now empty Zebes, and builds his power base, anticipating the day when he'll fight Samus again. Along the way, they steal an Aurora Unit, upload a backup of Mother Brain, and learn when Samus has taken the last Metroid. Cue Super Metroid, and another devastating death for Ridley. I guess from here it depends on whether we learn more in Other M, and whether or not the very odd looking X had indeed infected Ridley or just another of his species.
 * Other M maintains that it was the same Ridley...sort of

The Mother Brain of Super Metroid isn't the original, but a stolen Aurora Unit.
The original Mother Brain was toast at the end of Metroid/Metroid: Zero Mission. Samus blew her to hell, and the self-destruct system finished whatever that 80-odd missiles didn't. Moreover, at the beginning of Super Metroid, you travel through the original Tourian, which is still trashed from Samus' previous trip down there. Of note, Mother Brain's broken jar remains in place, which pretty much puts paid to the notion of her surviving.

However, Mother Brain had a backup plan - literally. Since Mother Brain and the Aurora Units are near-identical in terms of capabilities, space and power requirements, and operating platform (see above), it would have been trivially easy for the Pirates to steal another AU, install it in the rebuilt Tourian and load it with a Mother Brain "disk image." The Pirates also would have known from Metroid Prime 3: Corruption that Auroras can be mounted to all kinds of combat-capable vehicles, which inspired them to slap their "repurposed" AU onto that cybernetic body Mother Brain sports in the final fight of Super Metroid.

Samus keeps losing powerups because she's been selling them.
She never actually makes money from her little one-woman wars against the pirates, and, save for Prime Hunters and Prime 3, puts a lot of effort for no reward- and she no doubt has injuries, damage, etc, that need repair afterwards, as well as maintenance fees and such. Given that all the powerups are universally either Space Pirate prototypes or ancient artifacts, it makes sense that she would sell them after each adventure to recoup her losses, as, although she usually gets a personal victory, she really gets shafted financially each time, effort, time, and resources wise. She doesn't mind losing the firepower because she's Genre Savvy enough to know that she'll pick up new ones next time she really needs them.
 * It follows that the Chozo anticipated this, and set up the powerups all over the place as a means of providing for their surrogate daughter.
 * There's no evidence she ISN'T paid. I mean, she gets missions from the GF, and any group that would fail to pay our one woman army is really, really stupid.
 * When she gets involved with them, sure. But several times- such as Prime 1- she doesn't get involved (with them) at all, or like in Prime 2, the task done for them was minuscule compared to what she had to do overall- business sense dictates that price be agreed upon beforehand, so she can't exactly raise it because she felt like, say, helping the Luminoth and fighting her main/EvilTwin. And she kinda failed in Super Metroid, where she couldn't save the Last Metroid, which musta pissed them off given what they wanted to do with it.
 * And in Fusion, she outright defies them and destroys what must be billions of currency units' worth of research and technology. She even admits that she's probably a fugitive now.
 * Later games have gotten away from this trope entirely (Hunters) or come up with reasons why her power-ups are unavailable - broken by hitting a lift wall in Prime, suit-jacked by Ing and then in Prime 2,, hopelessly corrupted by X in Fusion. It's not a bad theory, but it's well on its way to being Jossed.
 * Ah, but in the start of Prime, before hitting the lift wall, she started off with nowhere near her full arsenal, so she must have sold off everything seen as nonessential. Same with the start of Prime 2, before the Ing attack. Then, not all of the gear attached to the Light Suit was Luminoth tech- quite a bit was stolen from Space Pirates, and wasn't there in 3. Finally, not all of her gear in 3 was, and it was still all MIA come her next mission.
 * Actually if Prime happened after Metroid 1, then her arsenal really wasn't that big yet to begin with. Granted she still would be missing a LOT, mostly in missiles, but her arsenal in the end of Metroid 1 was 255 missiles, Varia suit, morph ball, bombs, screw attack, high jump, long beam...(which she basically never lost ever after that...) and EITHER the Wave or Ice Beam (logically speaking only the Ice beam), since she couldn't yet stack them up. The hi-jump boots become the space jump boots, and she starts off with the Grapple Beam and CHARGE beam, which technically she shouldn't have even had "yet". So in an odd twist she may actually have started Prime BETTER OFF than she ended Metroid...save for the lack of Screw Attack and Ice/ Wave Beam. THEN lost it all to an explosion anyway.
 * This Troper was always under the impression that her powerups were breaking down from wear and tear. While she could repair the basic power suit, the stress of being hit by lasers and missiles and dunked in lava and acid and then gnawed on by all sorts of monstrosities was too much for the optional parts.
 * In Fusion, several major suit upgrades appear to be nothing but software. Perhaps the powerups are a free trial version?
 * I was under the impression it was just because the Fusion suit was biological and could be made to replicate weapons based on the download data.
 * I'm partial to the suit upgrades having a physical component and a driver component. The X infection had corrupted the software (stored in the organic components of the suit), which needed to be quarantined from the rest of the system. The downloads were simply clean versions of the drivers. It also fits with Zero Mission, in that Samus has the physical upgrades for the Grav Suit, Plasma Beam, and Screw Attack installed, but until she upgrades to the MK II suit, it simply wasn't capable of supporting those suit functions.
 * From the way a logfile in the first Metroid Prime suggests that Artifacts are carved specially, to the 'totems' that represent the powers of the powersuit's modules, this troper has formulated the not unreasonable WMG that the powerups really do take the form of emblems (Screw Attack), or statuettes holding emblems (Beam icons in Super Metroid). Thus, some of the lesser powerups may have been auctioned off to art collectors, and the older Artifacts may have stopped functioning after their material degraded too much due to the punishment Samus takes on a regular basis in combat or from environmental hazards (like the time her Missiles and Morphball failed in the first Prime - the force of being thrown into the eleavtor was too much for the old Morph Ball artifact plugged into her 'suit, so it finally shattered and was lost).
 * Perhaps Samus decides how many power-ups to bring to each mission beforehand. Having her suit damaged enough to lose them is a very real threat, so it'd be unwise to take everything every time. In Super Metroid Samus's original mission was simply to deliver a piece of cargo to a research station, not invade a Space Pirate stronghold, so she didn't suit up. On the other hand, at the start of Fusion, Samus was doing an Escort Mission on a planet she'd previously experiened the danger of, even without Metroids, so she went in with full equipment. Likewise, each of the three Prime games start with a much less hazardous mission than what each evolves into.
 * This troper theorises that the more powerful upgrades don't draw all of their power from the Power Suit, but are somehow at least partially powered by the planet where they are found itself, which provides a different form of energy than the Power Suit. Therefore, whenever she leaves, they'd be useless, so she just leaves them behind. Later upgrades to the Power Suit's core systems (such as the ones in Zero Mission's second part) allowed it to supply that other type of energy, so she could bring some of the upgrades that used it along with her. The ones she couldn't bring? They're designed with a security system that causes them to cease to function when they're no longer in the vicinity of the planet where they're found, so they're still useless if she brings them along, even if she already has the upgraded Power Suit. (I've posted the original version of my theory online somewhere else, and I have to check it again to see if that's everything, but I think that's it.)

BSL stands for Bioweapon Space Labs
The station is supposed to be a research facility to study the lifeforms of SR388, but how come it also contains a lot of Zebesian creatures? And how come they have a GIANT COMBAT CYBORG locked away in one sector? And then there's the whole Metroid breeding program. And would a research station really have a self-destruct system powerful enough to cause an Earthshattering Kaboom when the station is rammed at a planet? It's clear that the "research facility"-thing is just a front and the real purpose of the BSL is to act as a secret laboratory to develop new bio-weapons for the Federation. They obviously were studying lifeforms there, but not from just SR388. Instead they had collected various dangerous species from different planets so they could study them to see if they could be used as weapons. Nightmare was most certainly one of their finished products.
 * BSL certainly appears to be a rather unscrupulous military industrial company, but I also wonder if the Federation isn't their only customer. There are other governments in the series (the first examples that come to the top of my head are Egenion from Prime and the Kriken Empire from Hunters), and surely they would want weapons as good as the Federation's, if for no other purpose than to defend themselves if the Feds start encroaching on their territory. So, the Feds "own" the metroid and the X projects, but the Nightmare and the security robot might have been technology demonstrations aimed at selling those products to a larger market.
 * Nightmare's status as a BSL creation has been Jossed by Other M, although the truth isn't too far off;  Considering the large level of overlap between the stuff found on the Bottle Ship and the BSL satellite, it seems entirely possible that the latter was actually built to continue the experiments begun on the former, only under the guise of an innocuous "civilian" project, so that it wouldn't draw anyone's (especially Samus') attention

The Federation is secretly collaborating with the Pirates
Continuation of the above theory. There's a lot of Pirates on BSL, and they have Ridley's body in sub-zero storage. And the Federation seems to know an awful lot about Metroid biology all of a sudden. There are clearly some unscrupulous people in the Federation government, as the Metroid breeding program and their desire to use the X parasites as weapons proves. It seems likely that after the Pirate threat was largely neutralized (with Zebes destroyed and their homeworld located), some members of the Federation made some sort of deal with the remaining Pirates, gaining their knowledge of Metroid biology and bioweapon technology, as well as some biological samples (Ridley's body, or at least a clone, and the pirates seen on BSL). What the Pirates got in return and for what exactly the Federation needs Metroids, X parasites and other bio weapons they were clearly developing remains to be seen.
 * The pirates on BSL were X-infected doppelgangers like everything else. There might have been real pirates there before, but not necessarily.
 * The X might also have acquired knowledge of the Pirates back when the original Pirate raiding squad picked up its first metroids from SR388. Remember that X reproduce asexually and retain the DNA and knowledge of species they've infected in the past, hence any one X can mimic any species its predecessors encountered in addition to those it itself has encountered. One X infects a Pirate and goes on to reproduce; its progeny later wind up on the BSL station. Instant Pirates, just add water.
 * If the X infected a pirate way back then, why aren't there X parasites infesting all the pirate bases? The parasites don't just copy the host, they also devour it and spread to whatever's nearby.
 * Because the pirates have been breeding Metroids since the very start, and Metroids instinctively attack and destroy any and all X, microscopic, hosted, or otherwise. It'd be a cool mythology gag if it turned out that the hundreds of space pirates killed by Metroids while trying to train, study, or use as target practice, were actually attacked because they had X parasites in them. Of course, Metroids are aggressive enough that they'd probably attack regardless.
 * The Feds know so much about metroids thanks to the hatchling Samus turned over to them at the beginning of Super Metroid. They apparently had the thing under study for a good length of time before Ridley nicked it, long enough to discover how to apply its energy-manipulation properties for peaceful gain (quoted from opening text crawl), and they were smart enough to keep offsite backups.
 * See above re: Ridley as a species rather than an individual. The creature in the cryo-containment chamber was definitely the same species as Ridley, but probably wasn't THE Ridley.
 * But... he had the theme song!
 * I've added a WMG about that immediately below.
 * It's more likely that the Pirates either acquired their information by decrypting logfiles stolen from raided Galactic Fed vessels, or from a corrupt inside man in the GF ranks.

Samus never fought the real Ridley. She fought X parasite clones.
Think about this: What if the reason Ridley always comes back isn't that he's got a Healing Factor, or that he's being cloned or rebuilt or whatever, he's an X parasite. The original Ridley went to SR 388 to lead the effort to collect some Metroids, but was infected. He was able to somehow keep the parasites from completely absorbing him, possibly due to sheer badassitude. The parasites entered a symbiotic relationship with Ridley, gaining sentience from him in exchange for giving him a Healing Factor. When Samus fought him, he was already a hybrid, no longer the real Ridley. When she defeated him, he was no longer strong enough to resist the X, and they took over completely. The Ridley-X, which had also absorbed at least one Space Pirate, then reproduced, with one of the spawn becoming a Ridley and at least one becoming a Pirate. The Pirate-X then went on to cyber up Ridley-X, who Samus fought in Prime; he also constructed a robotic Ridley, or perhaps activated one the Pirates already had, for Samus to fight at the end of Zero Mission. All Ridleys fought since have been descended from this X. The body stored in the BSL station isn't Ridley, but a different member of Ridley's race, possibly the only surviving member after Ridley was X'd. It too is taken by the parasites, completely wiping out the species. This also means that: 1) Ridley will be Samus' eternal foil, and 2) that she's more prepared to fight him than ever, now that she's part Metroid.
 * One has to wonder, though. Given that defeated X Parasites simply return to their parasitic form when defeated, why didn't they just infect Samus upon Ridley's defeat (as the parasites from the Hornoad did when Samus first returned to SR 388 at the beggining of Fusion)?

The final boss of Zero Mission was a partially regenerated Meta-Ridley.
Chronologically speaking, it would be stupid to make the final boss a new character, because Ridley comes back as a cyborg in the very next game. There are some similarities between the Ridley robot and Meta-Ridley, like a multi-missile attack and a weak point in his chest, which the 2D incarnations of Ridley don't have. Ridley knew he was no match for Samus in this form, so he faked his death, started the self-destruct countdown and escaped to the nearest pirate ship: the Orpheon.
 * This troper believes that the Robotic Ridley was a kind of emergency backup. When Samus defeated Ridley, the pirates downloaded his mind into a robotic backup (the Feds have the technology so the pirates might have something similar too) while they sent a team to retrieve his body and put it back together.
 * Wait - there was a cyborg Ridley in Metroid 2? Since when?
 * According to the timeline, the game that comes after Metroid is Metroid Prime. Metroid 2 happens after all of that Prime nonsense is worked out.
 * Jossed: Apparently the Ridley robot is simply unfinished robot that Ridley wanted to be created in his image.

The palm of a Chozo's talons is an erogenous zone.

 * More than 80% of the time that you see statuary of a Chozo, it is either holding something or designed to hold something in its talons. These objects are usually round, allowing its talons to make contact with the entire surface. Such objects include but are not limited to powerups, the spheres at the end of a throne's armrests, the universe...
 * There isn't a single depiction of a Chozo rolling into a ball, yet it is one of the two most central design functions of the armor that they gave to Samus. Combine this with the reaction of many statues to the Morph Ball form, and it almost seems as if their main interest was giving themselves the ability to hold her comfortably in their talons.
 * The morph ball was probably a central function of the Chozo warriors' Power Suit. We simply never see one because Samus is the first "Chozo" in generations (possibly centuries) to choose the path of the warrior, and thus utilize the armor. Note that the Ruins Test at the end of Zero Mission appears to be wearing a form of the Power Suit, likely its original design, meant for an actual Chozo.
 * As they began to evolve past the need for material goods and physical forms, they became particularly philanthropist, spreading their inventions across the galaxy. One particular statue in Bryyo depicts a Chozo handing an object to a Bryyian. Perhaps for them, the most satisfying form of benevolence is to hold something in your talons and then give it to someone else.

As wonderful as the Chozo were, this recurring theme almost borders on obsession. Perhaps there is an underlying biological cause for it.
 * This theory has... Unfortunate Implications, considering the Chozo thought of Samus as a surrogate daughter, especially in Zero Mission where the talons are save points.
 * Not necessarily. It could be a bit like receiving a kiss from a family member, having someone rub your back, tickle your feet, clean your ear, or even having someone wash your hair. Pleasant, and a definite sign of affection, but not necessarily sexual.
 * Alternate theory: Given that Chozo are bird-like, one might assume that they lay eggs. Perhaps, for the Chozo, the natural way to care for/carry an egg is in their palms, which they curve around the bottom of the egg and carry close to their chest. As time passed, the symbol of a Chozo with their arms cupped around something became a symbol for protection and nurturing. The items the Chozo statues hold are their way of offering "protection" to their Hatchling. When Morph-Ball Samus sits in their hands, it's analgous to a child being cradled protectively by her parents. Or something.
 * Aww...
 * That is now part of this troper personal canon. Because, holy hell is it ever freaking d'awwww worthy.

The person writing the entries in the Logbook is Samus herself.
She's writing them for the benefit of anyone who follows in her footsteps, should she die in combat. This would explain where the tactical data on never before seen creatures is coming from, and why those entries always focus on how to kill them. She's probably compressing the information she downloads from the computers she hacks to what she considers the most relevant parts, as well.
 * This is possible, considering that, in Fusion, she does keep a "journal" of sorts... and the "voice" in both the logbook entries and the journal entry is pretty similar.
 * Some log entries include Samus' notes on particular creatures, upgrades, etc. in addition to the standard log data, so this doesn't entirely hold up. More likely, her suit and/or ship computers are doing the tactical analyses, to which Samus is appending her own thoughts.

Between missions, she likes to go clubbing.
Her off duty outfits seem to consist mostly of gogo boots, short shorts, and tank tops. Or less.
 * I can't justify the boots, but it seems possible that she's more comfortable in less-restrictive clothing.
 * Considering her post-Fusion thermoregulation problems in conjunction with the typical, ahem, female physiological reaction to cold, Nintendo's artists may want to get away from this image in the future. Or not.
 * It is entire possible that Samus needs to maintain a generous amount of direct skin contact with the inner layer of her powersuit, hence her liking for skimpy clothes. The Zero Suit was a specially made form-fitting suit that had the direct skin contacts inside its inner lining, and meshed perfectly with the powersuit's own skin-contact systems.
 * I'd say this is confirmed by the ending screens of Fusion and Zero Mission. Both show Samus in makeup and sexy outfits, in urban environments; in one case an actual bar. This troper just had this discussion with some friends, and thinks it makes her character more interesting. Instead of a female Boba Fett -cold, dark, and mysterious-, she enjoys a social life when she's not on a job. I mean, if Samus wants to look sexy, she really has every right to.
 * We have no idea what's fashionable in the Federation, since all we ever see are military personnel and other bounty hunters. Maybe the crop-top and shorts are just the "in" look this galactic cycle.

Samus is a former Bounty Hunter.
She started out using her power suit and weapons to bring in petty criminals to develop her combat skills, and then took on government contracts and Space Pirate hunting as a more lucrative enterprise (plus the whole saving the universe thing). She keeps the title for the same reason she was given it in the first place- it sounds cool.
 * That's a lot of backstory for her (apparent) age, considering she was also canonically a Federation policewoman, after being raised and trained by the Chozo, who also had time to become Precursors. Still, I suppose she had the time to bring in a few bounties, at least, and may continue doing so when there are no mercenary contracts to be had.
 * Maybe her Chozo blood slows the rate at which she ages, making her Older Than She Looks. She could be in her mid-40's, but physically and appearance-wise, she's in her late 20's.
 * The impression I had was that the Chozo were in a long period of decline. The Zebesian Chozo were sort of like late Qing China or the pre-WWI Ottoman Empireâ€”still prominent, but their heyday was clearly past. That decline might even have been the impetus for the Tallon IV colony, as an attempt to get back to their roots and reinvigorate their society. Certainly, the Bryyonian civil war seems to have happened a very long time ago, and the Chozo were depicted as still very much at their height during that time. So all the precursor stuff would have come and gone by the time the remnant rescued Samus.
 * Nope, she's still hunting. See the opening text crawl in Super Metroid: "Satisfied that all was well, I left in search of a new bounty to hunt..." However, it's probably safe to say that she doesn't bother with run-of-the-mill skips anymore; she would probably only take a contract if it involved some Most Wanted criminal or paid big bucks.
 * Or if the bounty is Ridley or the Space Pirates.

Samus and Gandrayda had a lesbian relationship
Perhaps this troper is reading too far into it, but the subtext points to this possibility.


 * As you walk into the GFS Olympus' briefing room in the very beginning of the game, Rundas and Ghor are standing around talking, while Gandrayda is doing her best Samus imitation - i.e. turning herself into a perfect copy thereof. The admiral yells at her to knock it off, and she breaks up laughing. Though you can't see Samus' expression, the fact that she doesn't go nuts upon seeing a clone of herself (and heaven knows she would have good reason to) argues that she's seen this routine before.
 * Alternatively, she could have assumed that, since there was a copy of herself there, in a heavily militarily guarded zone, and nobody else was doing anything about it, that it was perfectly friendly. Samus seems like the kind of girl who can keep her cool in pretty much any situation, regardless of how dire.
 * While trying to reactivate the second generator on Norion, you're assaulted by a squad of Phazon-enhanced Space Pirates. However, one of them turns on the others and kills them all, and of course, it's Gandrayda in disguise. She returns to her normal form and comments in a rather seductive voice that Pirate grey really doesn't suit her, and neither does machinery, so would you be so kind as to finish turning the generator back on? She then sashays out of the room with a wink and a "Thanks, Sammy," to which Samus just stands there gaping at her. What she's staring at is left to the gamer's imagination, but it probably isn't the generator.
 * Samus's reaction could be attributed to pure WTF at Gandrayda's attempt at flirting.
 * Gandrayda's atomic glomp attack. Need I say more?
 * Made even worse by the placement of her lower body relative to the victim's during said attack. Does This Remind You of Anything??
 * After you learn what the two functions of Gandrayda's power up do.  Not a turn on.
 * Not to mention, the Screw Attack is the quickest way to bring Gandrayda to her knees.
 * When Gandrayda
 * Samus seemed upset/angry enough to shoot (ineffectually) at Dark Samus when she.
 * Yes, but remember what Ghor and Rundas did.  While it is unsafe to presume Samus doesn't have a heart, I'm fairly certain any warrior worth his/her salt would be more upset at
 * Also note the emphasis in that scene with : all the focus is on Dark Samus. Samus doesn't really react at all until Dark Samus shows up, and she seems more angry that Dark is desecrating the dead than she is about the actual dead person. Contrast death scene, where the upset reaction starts before  is actually dead, and appears focused on  Dark's appearance is more or less an afterthought - this time Samus is upset over the death itself. Hmm.
 * This troper thought that was just Gandrayda being a bitch. What better way to remind Samus that she . Ending with was just downright sadistic.
 * Re: Samus' reactions, depending on how you look at it they're either survivor's guilt or a growing sense of grim inevitability. Four bounty hunters working for the Galactic Federation, all of them corrupted by phazon, and all equipped with PEDs as a method of controlling the corruption. Three of the four succumbs completely to the corruption, and the fourth is (at the time of the death of the third) also fairly heavily corrupted. Now, when Rundas is encountered and killed, it wasn't strictly clear that the other two had been corrupted, or if so then there might be a chance to save them. Ghor is encountered and reinforces the fact that they were all corrupted, and Samus fails to save him as well. Then Gandrayda is finally encountered, and also falls due to the corruption. Now Samus has just seen three good friends (At the very least, Hunters should have taught her that a bounty hunter not actively trying to kill her counts as a good friend) succumb to the exact same corruption that she's suffering from without any hope of being saved. Yes, it's likely that she's upset by those turns of events, especially since she doesn't have a crystal ball at that point that tells her that destroying Phaaze will cure her corruption rather neatly.
 * Samus doesn't really freak out and look away until Gandrayda takes her exact form. Who would want to watch themselves die?
 * I saw it in a much different way. When Rundas died she was too stunned by Dark Samus appearing out of nowhere to do anything but watch in horror as Rundas was absorbed. When Ghor died she was ready for Dark Samus to appear, so she bagan shooting, but that proved futile. By the time Gandrayda was dying she knew that there was nothing she could do.
 * Let's also not forget what Samus thinks at the end of the game. When she sits on
 * Considering that the scans imply that, whilst her age is is impossible to determine physically, she's mentally rather juveline, that adds a solid layer of Squick to this theory. Also, her mirthless killing of disloyal pirates makes her a very sadistic personality. BDSM much ? ... I wonder why I never realized all those implication (the juvenile Gandrayda becoming so sadistic and cruel as result of corruption, not the Les Yay) whilst playing. Then again, I played the Giygas battle without nightmares.
 * That's a key point. The in-game logbook notes that Gandrayda has a 'high degree of youthfulness'. There's no real homoeroticism present. Samus doesn't react, and Gandrayda makes a lot more sense knowing that emotionally, there's an eight year old in there. That's why the pet name 'Sammy'; Gandrayda is highly capable, but psychologically, she's a little kid. Notice how of all four hunters, she takes the mission the least seriously. And the random killings of Space Pirates? Kids pull wings off butterflies. Beyond that, we can be pretty certain that Samus didn't have a relationship with Gandrayda because Gandrayda is of unknown origin. Samus didn't know who Gandrayda was at the start of the game. Hell, Gandrayda is a shapeshifter from a completely unknown species. We don't know how her species reproduces, and considering how Metroid has avoided Rubber Forehead Aliens with such aplomb up to this point, who's to say they reproduce sexually in the first place? Combine that with her child-like demeanour and naivete and there's your explanation for any lingering doubts.

The Ing are Phazon-corrupted X Parasites from another dimension.
Dark Aether wasn't created by the meteor strike... rather, it has existed all along, there just wasn't a way to get there from Samus' reality. In the Ing's reality, there is no Samus, or perhaps she died before containing the X threat - at any rate, they've taken over the 'Dark Milky Way'. They've become smarter and more organized, what with their hive structure at all, and the general Ing template was taken from some native of Dark Aether able to stand the atmosphere there.
 * Take a look at their general morphology - especially the Ing Emperor, the number of legs, the way it moves.... Dark Aether is Metroid Prime's own separate copy of the planet, and just as God created Adam in His image, Metroid Prime created the Ing in Her image. Pardon the excessive religious metaphor.
 * This troper thinks they look more like evil, twisted versions of the Luminoth. Seriously, an Ing Warrior looks like nothing (to this troper) so much as a quadripedal U-Mos with tentacles on the back of his head instead of those two head-wing.. things. The more-advanced Ing might be something of a What Could Have Been for the Luminoth, perhaps.
 * This troper is convinced that the Ing are actually based off of the Phaz-Ing. Leviathans are stated to corrupt native lifeforms, luring in a particularly deadly one to be its guardian. However, Dark Aether likely had no indigenous life, so the Leviathan was forced to create its own, based on one of the Phazon-based lifeforms. The Ing in their final form was the result of exposure to Dark Aether's atmosphere combined with the highly mutagenic properites of Phazon infecting them. The fact that Phaz-Ing have a derivative name simply comes from the fact they were encountered after the dark Ing, but in fact preceeded them biologically.

The Metroid Prime/Dark Samus was a Leviathan Guardian.
It states in the that once leviathans reach adolescence they are launched at other planets inside a phazon seed. After impact, the leviathan enthralls and mutates a local predator to guard the core of the seed and then, leaving its shell to act as some kind of armor to the core. So Metroid Prime couldn't have been a leviathan, as the meteor struck over 50 years prior. When a leviathan hit Tallon IV in the first Prime, it enthralled a metroid. After its master, the metroid continued feeding on the phazon and eventually fused with shell/core, thus becoming the source of phazon on Tallon IV. This explains why there were
 * I think that scan was meant to imply that the creature on Tallon IV was an immature Leviathan - you'll notice that the scannable carapace in MP3 is found directly under an infant Leviathan, implying that the infant molted out of its carapace before cocooning itself. Perhaps the Tallon IV creature was the Phazon equivalent of a premature birth, being expelled from Phaaze while the Leviathan within was still embryonic. As a result of it having been "born" so small and weak, it could only corrupt one small area of the planet over a 50-year span, and the Chozo were able to seal it away with minimal difficulty. That may also explain the orange Phazon, too; the Tallon IV creature may have suffered from some congenital defect or birth trauma that made it produce abnormal Phazon in addition to the usual blue stuff.
 * I'm more inclined to go with the first idea, that Metroid Prime was a Guardian, a Metroid left behind by the Chozo, ensnared by the Leviathan, and mutated by heavy exposure to Phazon in the core. Its situation is mirrored by the Guardians in Prime 3's three planets - all four are local creatures corrupted to serve the Seed. Prime was just 50 years farther along. As for the scannable carapaces (there were two), I think the ridiculously heavy Phazon radiation on Phaaze had quickly mutated some of the Phazon Metroids there in the same way as Metroid Prime, and Dark Samus (who is Metroid Prime herself, lest we forget) killed them so that they would not be rivals to her power.
 * Following this, it would also be safe to assume that if Metroid Prime was the guardian of the Talon IV seed, the Emperor Ing was the guardian of the Aether seed.

Spire killed his own race.
We know Spire, the rock/lava dude from Prime: Hunters, is looking for his race, and is suspected to be the last one. Now go watch the begining cutscene of the game. The title one. Go on, Get your DS and do it. I'll wait. In particular, watch Spire's bit, where he rolls down the hill and smashses a few rocks. Note how he goes out of the way to smash them, and how the camera focuses on his face.

Here's what I think happened. Spire's crystals are possibly a deformity amongst his race, assuming the other rocks in the video are other Diamonts. He was shunned for this, and was reduced to hanging out with a bunch of similar rejects, taking drugs all the time, permanently off his head. Then some kind of civil war happened, and he went nuts. He went so over the top, in fact, that between the war and his murder, the population was quite severly reduced. He may have got ahold of some atomic weapons or similar and started pressing buttons, or, more plausibly, there never were many Diamonts in the first place - how does a rock race breed, exactly? He pried the Magmaul from someone's cold, dead hands and assumed someone had given it to him when the drugs wore off.

Therefore, Spire's intro movie depicts him killing the last few Diamonts whilst depressed, drugged up and crazy, and he doesn't remember it.
 * Apparently Spire's backstory was a reference to a cancelled game made by the same studio, so I doubt they put that much thought into it.
 * It was a game called Raven Blade. During a tech demo, a Diamonte-like creature is seen tossing a lava ball, likely the inspiration for the Magmaul. Spire's backstory is referencing the fact that Retro Studios (who apparently designed the Hunters) dropped the game to work on Metroid Prime, and he is the last evidence of Raven Blade left.

Metroid and the Kirby series take place in the same universe, at the same time
Well, Samus and a group of Metroids DO appear in Kirby's Dreamland 3...
 * And in Super Smash Bros. Melee's Adventure Mode, after Zebes blows up the camera pans over just a little ways to reveal Pop Star as the next area. Of course, it's Smash, so no assumptions, but still.

Going by the above theory and writing Popstar into Metroid canon, Metroids were inspired by the Kirby species

 * The Chozo did visit Pop Star once. They based the Metroids on the species' ability to suck in enemies, except it was more convenient to limit it to life energy and viscous organisms at most as Kirby's species can't transfer energy so easily. Fast forward, they returned and offered them some specimens, which were kept locked in some volcano and forgotten about, as they weren't able to cause much damage to the ecosystem. Too bad that prior to Metroid 2, Kirby wiped out the few remaining specimens.
 * Therefore, Kirby killed the Metroid franchise.
 * Except that Samus rewards him for slaying the Metroids.

Metroid and the F-Zero series take place in the same universe at the same time
Not trying to start a fad here. I mean this one. Couldn't Jody Summer and John Tanaka be employees of the same Galactic Federation that keeps contracting Samus?

Sadly, James McCloud's altered portrayal suggests that this series does not exist in the same universe as Star Fox. be a supercharged ray of plasma, but a falcon punch.
 * This troper has always wondered why Nintendo has two flagship characters that are Bounty Hunters IN SPACE, but never crossed them over outside of Super Smash Bros...
 * Well, one of them is a racing game and the other is action/adventure...ish. Not really compatable.
 * Put Samus in her modified ship. Easy. And James Mccloud could be a Legacy Character separate from Fox...
 * Putting Samus in her ship removes the adventure portion, and taking Captain Falcon out removes the racing. The two game types are not compatible. Samus should just make a cameo, if anything.
 * The game can be equal parts adventuring, railshooting and racing. Falcon would excel at racing and struggle at railshooting. Samus would excel at adventuring and struggle at racing. Fox would excel at railshooting and struggle at adventuring. And you can't say the three genres can't fit together in a single narrative. Remember The Adventures of Bayou Billy?
 * Fox struggle at adventuring... Oh right.
 * Since Metroid and F-Zero take place in the same universe now, in the next game, the charge attack/super missile for Samus' plasma beam won't

The Metroid DNA infusion has given Samus the power to eat life-energy like a Metroid.
Never explicitly stated, but I think it's pretty logical. That may be the whole reason Metroids can survive and even eat X Parasites - by draining their life-energy instead of simply ingesting the things, they truly kill them and don't allow an infection to take hold. Samus does the same thing in Fusion, and may, hopefully, retain this power in future installments along with her new sensitivity to cold.
 * Yeah, it makes perfect sense, but I'm not sure how it could be incorporated into future games.
 * 'Power Drain' attack? C'mon, use your imagination.
 * Well, a melee attack would be useful...
 * Or she could receive power-ups this way.
 * Actually, thinking about it, Prime 3's Grapple Voltage is a pretty good blueprint for how Metroidy energy drains could work.
 * If it didn't exist in every single game, it could have been a perfect explanation for the health powerups foes drop.
 * Actually, since the Chozo made the suit and the Metroids, the health is likely the same stuff Metroids eat. She's been doing it the whole time, only now she can do it outside the suit.
 * This is assuming Nintendo ever gives a crap about Fusion ever again.

In Metroid V Samus will lose her upgrades due to a virus
I mean this or the Other M method are the likely choices because the fusion suit is more biological compared to the power suit and going with the above theory she also use the life drain to get her powers back.
 * I dunno. The Rezbit enemies in Prime 2 attacked with a virus program, and Samus could basically Ctrl+Alt+Delete the virus away pretty easily.
 * That was a virus program though, computer virus. If Samus's suit has biological components it probably looks at hackers and EM Ps and says "***** please" before brushing them away. Now, the cybernetic components means organic viruses should be just as ineffective and yet organic parasites, the Ing and the X, caused it trouble so maybe a virus would work too.

The actual Ridley exists as a CPU program, and has had his mind uploaded into each of the Ridleys fought in the series.
It's highly probable that, if the Federation has mind-uploading technology, then the Space Pirates have something similar. The only question is when exactly this process began. Was it after the first Ridley's death in Metroid, or has this happened many times in the past? It may well be that Ridley's mind has existed for generations, serving as the Pirates' leader for countless of years. Regardless, this would mean that the final battle in the series could be against the Mother Brain-like Ridley CPU and an army of Ridley clones...
 * DO. WANT.
 * I have a similar theory. In a recent issue of Action Comics, the mind-controlling space catterpillar (yeah, don't think too hard on that...) Mister Mind is pretty much immortal not only through clones, but because even naturally, thoughts are transferred to the child. What if Ridley does this? Makes sense, considering how many times he gets killed and comes back as regular Ridley after resurrected Meta Ridley dies.

Phazon is a Eldritch Abomination, and "corruption" is its way of reaching into 3D space.
It's made very clear in the series that prolonged exposure to phazon can lead to death. When Samus uses hypermode in the third game, her corruption meter fills up unless she fires constantly. If her corruption meter were to fill completely, she would become a clone of Dark Samus. The Metroid Prime's final form in the first game could only be damaged by hitting it with beams of concentrated Phazon, the same subsatnce that Metroid Prime fed off of. This eventually lead to terminal corruption in the Metroid Prime, which killed it and allowed the phazon to manifest itself as Dark Samus. Dark Samus isn't the Metroid Prime, it is the projection of a monster that secretes phazon and uses it to project itself into our universe. The Ing in the second Prime are avatars of the entity that were created as a result of Aether's corruption and subsequent split into two different worlds. "Dark" versions of other species are undergoing the process of being assimilated into the entity's consciousness and transformed into copies of Dark Samus. The entity also seems to favor Dark Samus as a projection, as Samus has shown the strongest opposition to it thus far and wishes to match her power.

Ridley is a follower of Chaos Undivided.
Well, he is as brutal and sadistic as a servant of Khorne, he is described as being very intelligent, just like someone who worships Tzeentch, he is practically impossible to kill, an aspect of Nurgle...and about the Slaanesh part...well, let's just mention Rule 34.
 * Well, I guess that explains the hellish architecture he has in his lower Norfair lair in Super Metroid.

Save Stations work by cloning.
The flash of light/scanning is the station storing a print of your DNA. When sensors determine you've died, the station automatically recreates you from this data.

Sub-guessing includes:
 * Any Samus in any post-Metroid 1 game could be a completely different Samus from the one at the beginning of Metroid 1.
 * Similarly, the Samus that tells Admiral Dane "Mission Accomplished" at the end of Metroid Prime 3 might not be the same one who defeated.
 * So it re-creates the entire suit with all the upgrades as well? Sorry, I don't buy it. Besides, they are explicitly referred to as "suit maintenance" by NPCs.
 * The stations might include homing beacons for a short-distance teleportation system, which could haul you out of trouble if your suit is critically damaged. They might even use the same mechanism as the freefall recovery system (teleports you back onto last touched platform if you miss a jump).
 * It's likely that in-story, the save stations are just used for maintenance, since Samus has never canonically died, or missed a jump and fallen into a bottomless pit. Obviously, we as gamers are not nearly as good as the canon Samus, and so need such saving graces to prevent the game from becoming unwinnable.

The SA-X fought at the end of Metroid Fusion is half-Metroid
The SA-X at the end of the game is a mutant hybrid between an Omega Metroid and an X Parasite that attached itself to Samus's Power Suit. It's final form is it's true appearance, the freakish result of an X taking over the Omega Metroid's body.
 * The Metroids are the main predators of the X. Any X would be absorbed just by touching it. It is impossible for X to infect a Metroid. The final form looks more like a mash up of all the forms the X have taken rather than an Omega, anyway.
 * This troper always thought that SA-X's One-Winged Angel-esque form kinda looked like a Biological Mashup between the Power Suit and a Hornoad--which is consistent with the fact that when Samus is infected at the very beginning of the game, the X Parasite that did it came out of Hornoad that Samus shot with a missile.

Samus is the next Hero Of Time
To back this claim up, Orange is the new Green, and the Screw attack is part of the Triforce.
 * Hylian is a mutation of High Land and Samus is one of Sheamus, giving them both common Irish roots.

Two things about Adam

 * 1) Samus' gunship is not just an upload of Adam; it is Adam. In the manner of The Ship Who Sang, the computer actually uses the recovered central nervous system of Adam Malkovich as its CPU. This is particularly likely because there are no non-organic computers in the Metroid series, but plenty of computers and robots with organic cores; both the Aurora Units and Mother Brain are organic, and even robots like B.O.X. in Metroid Fusion have organic cores for no readily explained reason. It seems likely that non-organic computers either cannot be built (perhaps the Metroid groups don't know how to), or there are laws or other restrictions explaining why they don't. There's ample precedent for injured war heroes having their brains recovered and used as the central components in robotic bodies, as both Ghor and Weavel demonstrate, so depending on the circumstances of Adam's death, which remain unknown we know from Metroid: Other M, it's entirely plausible that it's actually him in there.
 * It's never said that nonorganic computers don't exist. We see plenty of smaller terminals scattered throughout many of the technological areas, and no sign that any of them are biological in nature.
 * There are non-biological computers, the biological ones are just much more powerful.
 * Er, terminals and the like are fine, but I was thinking about intelligent A Is. The only non-biological computers are 'dumb' computers, which store data but are incapable of acting on their own. All intelligent computers seem to be organic. True, it's never said that they have to be, but there is a pattern, and as this is Wild Mass Guessing, who needs conclusive proof?
 * 2) Samus and Adam had an intimate relationship. Certainly Samus seems closer to Adam emotionally than she does to any other character in the entire series (save her parents and some of the Chozo in the manga), and they seem very familiar. We don't see Samus getting close to or feeling truly comfortable around anyone else. Adam appears in the earliest Metroid canon chronologically, in the manga. He looks set to appear in the flesh in Other M, set after Super Metroid, so we know Adam didn't die in the battle in the manga. And then he appears in Metroid Fusion, the final game. I imagine an on-and-off romance between the two of them that runs throughout the entire series, beginning to end. It's a sweet thought, isn't it?
 * Yes, especially if Adam gets a new robotic/partially organic body.
 * I always interpreted their relationship as nothing romantic and more like Adam was a paternal figure for Samus. Keep in mind, just from what we see in the manga and the Other M trailer, Adam was much older than Samus (although far be it from me to stand in the way of a good May-December Romance), and met her when she was in her early to mid teens. Just from the manga and his revelation speech in Fusion, I got the idea that Adam was a tired old veteran who had given up hope that the war would ever end, until he met Samus and she restored his hope. At the same time, from his last conversation with Samus from the manga, you learn that Adam was pretty much the last person left in the universe who saw Samus as more than a tool or a weapon, and was worried that in slipping too much into her lone wolf warrior persona, she was losing herself. ("Remember that you're a lady. That's something that's lost on you lately.") The manga also shows that Samus was a hotheaded, rebellious teen (like most teens) who didn't like listening to authority figures and didn't seem to understand just how much trust and leeway Adam granted her. Not until it was too late, and he was gone, if the reflections in Fusion are any indication (and even there, Samus originally notes that it's his abrasive commanding tone that makes her associate the AI with Adam, possibly digging up memories of their relationship when she was a kid. As she reflects on it more, her memories of Adam become more positive and respectful).
 * Unfortunately for the romantic aspect, Other M seems to have put paid to that idea, with Samus repeatedly referring to Adam as a father figure. On the plus side, just about everything in the above paragraph was confirmed. And either way, she still cared very deeply for him in one way or another. As for his nervous system being recovered, though, it seems unlikely given that

Ridley is telepathic
When he "talks" in the manga, he is telepathically sending messages through others' minds. In the games, he does nothing more than growl and grunt.
 * Could just be that Ridley, unlike a lot of villains, doesn't see much point in chatting it up before he tries to kill his foes. Hell, maybe that's what his All There in the Manual super intelligence is referring to - he's Genre Savvy!
 * Heck, that would explain why he's conveniently waiting for Samus at the Artifact Temple in Metroid Prime. He knew that Samus would collect all the Artifacts, and so waited at the temple for her to unlock the Cipher so that he could kill her and gain access to the Impact Crater (it would have worked to if he had kept his big mouth shut).

The Chozo were capable of using Morph Ball.
This would explain all of the convenient Morph Ball-activated pathways, puzzles, generators, and traps everywhere, especially since the Chozo apparently had civilizations most everywhere Samus has visited so far. We know Samus was infused with Chozo DNA, which is how she got some of her superhuman abilities, and they designed her suit for her. The manga shows that the Chozo themselves possessed armor not unlike her own. Morph Ball is only unique to Samus now, with the Chozo all gone (or if any remain, their fate is largely unknown), and why it wouldn't be something you see every day.
 * That seems to be fairly obvious. I mean, why would they have build Morph Ball shrines on at least two of their worlds if they couldn't use it themselves? Plus, it's been mentioned elsewhere that the Morph Ball was originally used as a meditation aid by the Chozo.
 * The only place the "meditation aid" thing has ever come up is in the fancomic Metroid Third Derivative as a fanon explanation for it.
 * Confirmed by this picture from Zero Mission artwork.
 * Also confirmed via Fridge Brilliance in Prime 2: Echoes. Whenever the Power Suit reboots, the BIOS lists various information relating to the restart process. This includes the Power Suit's model number: "Chozo Battle Suit ver. SA1-4468-VM6-P" Therefore, it's a Chozo Battle Suit specially designed for Samus Aran. This means, by extension, that there are also Battle Suits designed for Chozo warriors. As the Morph Ball is compatible with the Power Suit, logic dictates that it should be compatible with all models of Chozo Battle Suit; it appears to work by turning the user into energy and containing them within a two-piece shell, so there's no reason it wouldn't be compatible with all Battle Suits.
 * Seconded. One of the life paths that young Chozo are offered is "Warrior". Samus was merely the first to choose that path in a very long time. Generations earlier, it was likely that there were many warriors, who wore Power Suits like Samus'.

Samus knows where the last remaining Chozo are.
She doesn't search for them... and also doesn't tell a soul. There's a Hidden Elf Village out there somewhere that is trying its hardest not to get wiped out again.
 * Knowing the Chozo, they're preparing to wipe out the Space Pirates. Or, just observing and making minor adjustments to the universe. I'd feel sorry for anyone that tried to wipe them out.
 * Knowing the Chozo, anything that wipes them out will propably do so purely by accident. It seems that the Chozo lifecycle is: Find a planet, settle on it, scatter a few relics for the protagonist in a videogame to find and make use of, and then get their shit utterly ruined by Space Pirates/circumstance/their own meddling, any survivors repeating the cycle. Seriously, name one planet that has had any significant Chozo presence that hasn't had the local chicken population utterly decimated. Zebes, SR388, Tallon IV, Elysia, Bryyo... The Chozo landing on your homeworld is pretty much indicative that something horribly, horribly, horribly terrible is going to happen in the future. Samus Aran, Destroyer of Worlds? Pfah, the Chozo tend to royally mess up planets without firing a shot. No, if there is a hidden Chozo planet out there, it's already Doomed.
 * Judging by public opinion of the Chozo, it sounds like their influence converts every civilization they meet to Too Good to Last status.
 * Since you asked: The Zebes colony were pacifistic and had less than 50 Chozo there, and most of them left before the Pirates got there. SR388 never had a Chozo population, they dumped the Metroids and some defenses (that metroids couldn't bypass) and left. Tallon IV was circumstance, but they solved the problem while ascending to a higher plane of existence (they left). Elysia, they built some robots and left. Bryyo, they gave some advice and left. In nearly all of these instances, no Chozo actually die, and they weren't there at the time. However, the universe has it out for them, and their record implies they themselves have escaped it every time. This hidden colony is already empty, and whoever finds it is the one that is doomed. The Chozo are Doom Magnets, but they have realized this and have ceased all contact with anyone.
 * My thought is that as long as there's no trouble, there's no game about it.
 * It might not be that they're avoiding people intentionally, although it seems likely if they're Doom Magnets to the Nth degree. The manga and other places in the games state that the Chozo are nomadic. They don't have a homeworld and don't believe in co-opting another planet as their own unless it's only temporary (the ones on Tallon IV took it to its extreme and refused to disturb anything during their stay). Their colonies are only established long enough for them to accomplish what they intended, and then, as stated, they leave. Elysia was where they built an observatory, and they constructed the Elysian drones to maintain it so that they could leave; Zebes was for bioresearch and bioengineering purposes to create things to protect the universe, and while its possible adopting Samus caused them to stay longer than they intended, I have no doubt they always intended to leave even before the Pirates ran them off (as for Mother Brain, Elysia also had an Aurora Unit. She was probably as much for Federation use as theirs); Tallon IV was where they stopped for meditation and to learn about living in tune with nature to ascend to a higher plane of existance. So it might not be so much that they're being driven into hiding so much as they're just naturally like that: a nomadic race that pops up, does its job, and fades into the night until they do it again.
 * Alternatively, the Chozo no longer physically exist in the galaxy, but have all transcended.

Sylux is an AI
As such it has no gender and "it" is an acceptable pronoun.
 * A great possibility, to be sure, but Sylux's main shtick is that no one know anything about it. We know it hates the Federation and Samus by association, and that it comes from Cylosis. And uses GF technology. Someone else would have to be behind it, as the armor design is too recognizable. That person is likely the real Sylux.

Sylux was the prototype for the mind-uploading program.
Sylux was originally a member of the GF who was selected to have his/her mind uploaded (like Adam, he/she was probably a high-ranking member of the military). It was decided to upload his/her mind into a suit, so that Sylux could continue physically as well as mentally assisting the Federation. Something went wrong in the process (perhaps the suit was partially organic like Samus's and messed with or destroyed Sylux's mind), leaving Sylux a wreck of its former self. Then, Sylux either swore vengance on the Federation for corrupting its mind, or the suit's AI is Ax Crazy and is fixated on the Federation because that's where it was constructed. Samus would also be a main target for her prior assistance of the Federation. (Yeah, this is kinda out there...)

Sylux is a result of the Living body arms development lab shown in the Other M trailer
It gave Sylux powers similar to Samus, but something went wrong in the experiment, giving Sylux a reason to despise the Federation
 * That actually makes sense, and would justify her anger at Samus, if she's the same person who dies in Other M.

The Power Suit is powered by Getter Rays
Hence why the Varia Suit looks like Shin Getter 1 and why Samus can change shape and use the Shine Spark. As an extension of this theory, Samus will eventually gain the ability to combine with a fast, blue-white Hunter and a heavily-armoured yellow one.
 * Could the first be Sylux?
 * And the second Kanden? Most likely though, this will happen via her just killing them and assimilating their armor. I don't know about Getter Rays, but evidence suggests the suit runs on life energy; the Chozo were adept at manipulating life, as evidenced by Metroids eating it.
 * It should also be noted that Samus's first Power Suit (whose Varia mode was a Palette Swap rather than having giant shoulders) bore a closer resemblance to the original Getter-1, and that according to Word of God the "Legendary" Power Suit which replaces it in Zero Mission can only be used by people with strong willpower.

Samus is of Irish Descent
Samus and Aran are both Irish names - Samus being the feminine version of Shamus, which makes Samus Is a Girl a rather obvious trope. Aran is also a traditional unisex Irish name that Nintendo somehow thinks is a non-standard spelling. Earlier versions of Samus' armourless sprite depicts her as a redhead rather than the blonde she is now.
 * It was more brown than red (at one point green) and the NES cannot do the color yellow well. Princess Peach used to have a similar hair color.

Metroids arent extinct
Due to one or all of the following, Metroids weren't truly wiped out in Metroid 2 and Super Metroid.
 * 1) The Space Pirates were breeding Metroids and carrying them along all over the place throughout the Metroid Prime Trilogy, and it seems unlikely that Samus would happen upon every single Space Pirate expedition and base containing Metroids prior to Metroid II.
 * 2) As referred to above, the Chozo aren't really extinct either, and so continue to breed Metroids as a safeguard in case the X get loose.
 * 3) The destruction of Phazon canonically didn't instantly kill corrupted beings, as demonstrated by Samus herself. There's swarms of Phazon-enhanced Metroids that revert back to normal Metroids post-Prime 3.
 * 4) It's not like Samus killed every single non-Phazon corrupted Metroid on Tallon IV, either.
 * Though most of these are on Elysia, where they have very little in the way of live prey.
 * In addition, even the Galactic Federation has backups of Metroid DNA and BSL certainly wasn't the only installation.
 * It is always a possibility that the entirety of Metroid II isn't the only act of destruction the GF are doing. They might have just sent Samus on the most difficult eradication mission, where teams are sent to other parts of the galaxy to clean up other remaining Metroids.
 * All this proves the second game's plot hole. The Pirates intercept ONE load of the parasites and then the federation decides Metroids need to die forever? The Prime trilogy adds populations of subspecies in several different places throughout the setting. Our shero doesn't get around to exterminating them completely either. The whole phazon thing sends the pests flying through space and even when phazon is gone there are still a bunch of flying parasites all over the Federation. That's what happened between the first two games that made the Feds decide they wanted the pests gone forever! Since the ones from the planet SR388 are tougher than the strains elsewhere, they send Samus to deal with the toughest.

Gorea was actually a Chessmaster
Gorea is already an established psychic, able to send telepathic messages across galaxies. When he came upon the Alimbics, a race of psychics, he began to kill and absorb them to become more powerful, absorbing weapons in addition to this. Throughout this entire ordeal, the Alimbics had something that could kill Gorea: the Omega Cannon. However, instead of using this awesome weapon, the Alimbics all opt to kill themselves in order to seal Gorea. They even seal the Omega Cannon in the same inter-dimensional prison. It's then revealed later than Gorea is able to draw more power from the Seal Sphere, the very thing he was sealed with. So here's what I think happened:

Gorea realized the threat of the Omega Cannon and sought to stop it any way he could. He did this by tricking/minraping the Alimbics into a state of severe hopelessness and convinced them that the best way to get rid of him would be the "kill ourselves to seal you" plan described above. So the Alimbics transfer their psychic essence to the Seal Sphere and place him in a space between dimensions. He also convinces them that the Omega Cannon is far too dangerous to use. At this point Gorea has gotten all the Alimbics into a small area that he can eat at his leisure, and time to study the Omega Cannon. He even had a back-up plan: send his extragalactic psychic message to get someone to release him. It would have worked, too, if he hadn't inadvertently called Samus.

Samus is older than she looks.
Samus is actually somewhere in her mid-20's during the events of the original Metroid, as supported by her model in Metroid Prime. Given advances in medical technology and her distinctly weird genetic makeup, she might actually be even older. Don't care if it's been Jossed, Nintendo; there is no way she was frickin' 17.
 * Alternatively, maybe she was 17... in Zebesian years. This troper hasn't read the manga (yet), but if years are longer on Zebes than on Earth, Samus could have been 20 or more Earth years old, but still technically 17. Or maybe it's K-2L years that are longer than Earth years, and she uses them instead of Zebesian years or Earth years to determine her age. Or maybe this troper is too much of a nerd for his own good.
 * It makes more sense for her to have been still developing as a teen while and suspected of as male for the simple fact that she was flat and more muscular than anything. Plus, the way the series is pretty far set apart. By the end of the game series so far, she has to be pushing late 20s to mid 30s. What you should really bring up is that she disappeared for a few years before her first mission after serving with GF. Meaning, she knew Malkovich when she was 14. Ship that.
 * Even if flat and muscular, females have a different body type than men...but then the right clothing could obscure that, perhaps the police uniform did.

Metroids are docile and friendly at birth, at least towards the Chozo
Almost all of the Metroids in the games are either raised by someone evil, a military organization or just in the wild. There is one Metroid that had something that didn't immediately try to murder everything, and that's the one that imprinted on Samus. Although most metroids from dangerous backgrounds are simply raised to hunt, this Metroid imprinted on Samus, something that hasn't seemed to happen to anybody else. Metroids were created by a peaceful race to stop a parasite. It stands to reason that anything they would create would be tameable.
 * This is all but confirmed by official canon. It was even mentioned in one of the games that using the gamma rays that the Space Pirates used to mass-bread them is unsafe because it just really pisses them off.

Hunters plays a bigger role in the story then we may think
Several hints seems to point this out:
 * Sylux: They are slowly making him/her/it The Rival to Samus. Think about it. He's a bit on an Evil Counterpart (yet he's not an Evil Twin, like Dark Samus or Sa-X). Sylux will be a Foil to Samus. His ship appears in the 100% ending of Corruption.
 * All the characters in Hunter have a trophy in Brawl.

The Chozo Planned Everything
Ok, bare with me here. We know the Chozo are able to see the future, or atlest snippits of it. With that in mind, when they found out about the X Parasite they decided to do something about it. So they decided to make the Metroids, which means "Ultimate warrior" in their language. This is all well and good, but they put a major weakness into their Metroids. A weakness to ice. From a normal standpoint, thats them avoiding their creation turning on them and being indestructible. But consider this.

Later on, in Fusion, Samus must be infused with Metroid dna, making her have their weaknesses. A weakness to cold. She gets something LIKE the varia suit in that game, protecting her from the cold, but not letting her use the ice beam. But at the end of Fusion, SA-X makes a sacrafice, giving its true varia suit to Samus. As such, Samus can use the ice beam now, despite being a Metroid. In essence, she has become a Metroid that is completly indestructible. She also destroys the X Parasites completly. Which is exactly what the Chozo set out to do.

Talk about foresight on the Chozo's part, huh?

The title Other M has nothing to do with another Metroid.
Rather, it's related to the overarching topic of the game. Let's consider some of the stuff we know so far: A little girl is a "major character" (though she's not related to Samus). The openining harkens back to Super Metroid, and captures both the hatred and destruction of a certain Brain and Samus' horror at the death of the baby Metroid. In a recent gameplay trailer, the opening shots show something that can only be described as a fetus. As for the title?
 * Reading this preview,  I'd say that you're right.
 * A space Action Girl extremely Badass kicks asses and has a sweet spot for children? Never heard that one before...
 * Mostly confirmed within the finished game: maternal themes are still very important, both in terms of Samus' connection with the Baby and

The Space pirates look so different from game to game because they keep genetically modifying themselves
Each time Samus defeats the space pirates, they attempt to improve themselves genetically in the hopes that the next time they'll become strong enough to defeat Samus. Hey, it makes as much sense as any other theory...
 * The Prime games outright say that the Space Pirates are constantly bio-engineering themselves, explaining why they are dozen different types of pirate per game. Making this neither wild nor a guess.
 * It's also possible that the differing appearances are the result of different phenotypes of the same species, or even of different equipment (and in the case of Prime 3, Phazon mutation).
 * It's also said the the pirates aren't one species, just a collection of different, notorious species working together. It may just be that when one species gets annihilated by Samus, they bring out another. Makes sense considering how long they were around, and that the end of Prime 3 pretty much spelled death for most of them.

The Arans are realted to the Roivas family
Because Samus has far too an uncanny resemblance to Alex (they even share a voice actor).
 * Remember me, Alex?

Samus doesn't swing that way. Or the other way.
Having been raised, and genetically modified, by the Chozo, Samus has no physical attraction to members of her own species. And since the Chozo are either extinct or departed forever, there will never be a romantic sub-plot in any Metroid game ever.
 * Now you're just asking for a Copy Cat Relationship Sue to show up. But seriously, I don't think her genetic modifications, or being raised by Chozo is quite enough to completely eliminate all biological urges. Knowing her luck, she probably runs into No Guy Wants an Amazon.
 * Could be worse, though. I forgot to take into account her newly-acquired biological modifications in the final installment. There's an uncomfortable amount of Samus-Metroid shipping on the internet.
 * This could be true, since she was taken up by the chozo pretty early. Psychologically speaking, emotion is derived from labels we give to certain things. If Samus never learned to get...excited, shall we say, by certain parts, it's doubtful she ever would.

Metroid V (when it's finally made) will turn everything on its head
The Metroids are all but extinct, (there's gotta be traces somewhere) the Space Pirates seem to be a shadow of their former strength, and the Galactic Federation might be on the verge of getting too powerful for its own good. The next game will have Samus on the run, both her and Adam being wanted for the BSL incident after having witnessed what the Federation is willing to stoop to.

Now, Samus will have to ally with her former enemies, and fight her former allies. She'll have to either excise or embrace her Metroid DNA, which may be able to grant her new powers and abilities, and perhaps find an unlikely ally in the remnant of the Space Pirates, whose position as her enemies is now taken by the Federation soldiers sent to take her down. (and maybe other bounty hunters sent after her) She might even have to seek out the Chozo to help her.

It's even possible that the Federation still plans to try to weaponise the X-Parasites, (and we thought the Space Pirates science team had vapor for brains) which may have to be countered by cultivating Metroids to strike back against them. And who has the facilities, the know-how and craziness to breed Metroids in captivity?

And I'm quite sure that Nintendo isn't going to just let one of their lucrative franchises sit with No Ending, especially since Other M is looking to add more foreshadowing for Fusion. And they should know better than anyone that 2D games on home consoles still sell in the millions.

Ridley is a Federation spy
At some point after leading the attack on Samus's home planet, Ridley defected to the Federation, and has been deliberately sabotaging Space Pirate security ever since. This is both why Space Pirate security systems seem to be custom designed for Samus (that is, they actually are) and why Samus has yet to finish him off permanently.

Samus is sterile
After all the genetic mucking about she's had done to her, I wouldn't be surprised. Even if her eggs have been miraculously untouched after she had been given chozo DNA, infected by X DNA, cured with metroid DNA, and absorbed the DNA of everything ever absorbed by any X she absorbed, her reproductive system is probably not untouched.
 * Either she's sterile, or any offspring of hers will be a horrifying/AWESOME hybrid of human, X and metroid, growing up to become an unstoppable warrior.
 * Don't forget about the horrific mutations (and associated potential superpowers) caused by genetic damage from prolonged phazon exposure and corruption!
 * You All Fail Biology Forever. Samus is a woman, and so was born with all her eggs pre-forged. Her kids will be half-human, half-whatevershefucks if Nintendo stretches the laws to Gohan levels. Most-likely they'll be purebred humans, if they ever exist at all! The Phazon corruption-induced sterility is a definite possibility, radiation and whatnot. And she was infected by X parasites, not X DNA.
 * There's no telling how being infected with DNA from sci-fi aliens with only vaguely-explained properties would affect a human being's ova. Under normal circumstances, yes, the only real options are that they're unaffected, sterile, or mutated from radiation, but for all we know Metroid and Chozo DNA could've gotten into them somehow.
 * Actually my point wasn't about her eggs, though who knows what they've been through. My point is that her body might not even have the right hormonal cues or possibly even physical mechanisms to carry a child to term anymore. While she at least outwardly looks fairly normal, the endocrine system is a delicate thing, and her genetic alterations, with one possible exception, have never been really gentle.
 * The Expanded Media for Super Metroid (As well as Other M itself) suggested Metroid: Other M shows that Samus had a strong, affectionate relationship with the baby metroid, like it really was her child. Since the metroid had chosen her as its mother, it's possible she is finally letting loose the repressed effects of her (once thought to be pointless) biological clock.
 * Even if she's not traditionally sterile, the Metroid vaccine would probably have enhanced her immune system to take care of, not just X, but any parasitic infection. Even if she managed to conceive...well, we've seen what happens when a fly hits a bug zapper.
 * This troper thinks that Samus will probably reproduce the same way that a Metroid does, now that she's got their DNA.
 * By laying Metroid eggs?
 * Or Chozo eggs, or something partway between the two. Either way, they'll probably need external fertilization by a compatible male.
 * That reminds this troper of some rather disturbing fan art that involved an exhasted Samus sitting near a load of unhatched (presumably metroid) eggs.
 * I actually meant multiplying when exposed to beta rays.

Castlevania Sorrow is to Castlevania as Metroid Fusion is to Metroid
There are an astonishing amount of similarities between the plots. A Metroidvania with a new style of play, wherein you can absorb your foes after defeating them. In both, you are what you used to fight, Soma as Dracula and Samus as a Metroid. In the end, Samus fights a copy of her suit, and in Dawn of Sorrow, Soma fights a person who copied his powers. Aria of Sorrow and Fusion were released on the GBA, roughly around the same time.

What does this mean? In the Sorrow games, Soma was attacked by a Belmont when it was revealed that Soma was Dracula. Perhaps in a sequel, (as suggested by someone above) she will be attacked by her former allies and bounty hunters for being a Metroid and for destroying BSL.

This time, maybe detonating a planet won't be the solution. Oh, who am I kidding?

Samus' Metroid DNA actually offered no incompatibilities with the Ice Beam
The federation made it up in a similar way to the Plasma Beam, so that she would not become more powerful and not kill either the SA-X or any of the Metroids. She could have absorved it and assimilated the ability like any other X with data, but it escaped through the crumbled emergency exit before she could have a chance of getting it. When she gets it, her suit turns orange... as it probably also had color data. Or something.

If Metroid V is ever made, Samus will be getting along just fine with the GF
She has a history of blowing up whatever place she's sent to and they still keep hiring her. In Hunters she's described as their champion. She has a reputation that seems like a cross between a Memetic Badass and Shrouded in Myth. Maybe they'll offer her a little more leeway to explain herself than she thinks? Perhaps they'll just make that game's plot her carrying out some "community service" or taking a job to pay off the bill for a new space station?


 * Even if they're okay with her, she won't be too happy with them.
 * Destroying their research station and a planet really doesn't sit well with the Fed, so Samus goes in search of other employers and bounties out of their territory, allying or renewing rivalries with the other bounty hunters. People working on the case just can't help but ask how Samus destroyed the SR388 the way she did though. An investigation reveals much illegal activity and several people get fired or put in jail. When one of her missions inevitably gets linked to a crisis, Samus must re-enter Federation space in a weakened state in range of an Olympus class battleship. She knows this will mean imprisonment or death but does it to save the cosmos. Instead she gets a shero's welcome and is publicly pardoned. Many rogues in the Federation still want her dead and the time she was completely at odds with the Federation still becomes the focus of many games. Their relationship is never the same but Samus does reconcile with them eventually.

Sylux isn't evil
What indication do we have that v is evil? That Sylux hates the Galactic Federation, attacking their troops and taking their stuff? Remember that it is a group which has been shown to be not very nice itself in Fusion (V even only opposes Samus because she works for them) and the 2nd part is nothing Samus doesn't do to her own enemies (Space Pirates) all the time.

Anthony is Pikachu

 * So, the Pikachu from Brawl later underwent an extreme, experimental form of evolution (maybe it involved Higgs bosons), that he could be the same species as his savior? ...Makes about as much sense as anything else in OM's storyline, and is significantly more awesome.

Ridley has "genetic memory"
This may explain how in Other M,

Ridley was a ghost
Whenever he gets cloned, he rejoins his body like nothing happened. Presumably he must have learned that trick from Mother Brain, who would know all about the Chozo's ascension. What? It makes as much sense as nanomachines!

Ridley is not a Space Dragon, he is a Space Phoenix
While Ridley is known to have a healing factor, it is not good enough to save him from complete destruction, often via bodily explosion (ie: bursting into flame.) But, it is now known that Ridley has several developmental stages, which mature at a ridiculously fast rate, apparently tied to flesh consumption just like his healing. If Ridley is in fact able to rise from ashes, taking the form of a harmless creature that nontheless can tear a human to pieces would be a perfect way to escape, especially since it seems to retain his intelligence. This would allow Ridley to live indefinitely, being reborn whenever killed, and possibly allowing him to gain new abilities (like the cloaking he does in Super Metroid) or become stronger, depending on how he chooses to have his immature forms develope. While he isn't exactly on fire constantly, his fire/plasma breath could be a result of his nature.

All the "infesting" villians are the same thing
Presumably, there is an Eldritch Abomination that seeks to corrupt the entire universe. It's first attempt was Gorea, but it was sealed away. It's second attempt was the X parasites, but the Chozo made Metroids to stop them. It's third known attempt was the planet Phaaze and the leviathans. It's final attempt was the Kriken Empire. It was probably responsible for killing off Spire's species.

Sylux and Samus will team up
Sylux hates the Galactic Federation, and Samus is likely an enemy of them since the end of Metroid Fusion. In the next game, they'll team up together, and then Hilarity Ensues as Sylux keeps trying to betray Samus but fails.

Samus is doing a Self-Imposed Challenge for Other M
Even in the beginning Samus is equipped with far less than her usual arsenal, maybe she just wants to give herself more of a challenge? when Adam shows up she decides that she will put the decision on him because she can't trust herself not to get pissed and equip everything and break her run?

Adam is being Genre Blind on purpose
Adam and Samus obviously parted on less than the best of terms, maybe when he sends her with less than ideal equipment it's to make sure she doesn't feel like she can get away with everything anymore (which isn't to say he's trying to hurt Samus, he knows she can handle it, and, in sector 3 for example, when it gets too much for her to handle, he relents for her safety.)

Samus is on her period in Other M
She's obviously been having a less-than stellar couple of weeks, what's one more humiliation on the pile. (this also has the effect that that while her characterization is her own, it's a bit exaggerated for the plot.
 * It's not really exaggerated, you (by which I mean everyone who has a problem with the Other M side of Samus) just figured she was a hardened, unfeeling person.
 * Because we all know the only personalities a woman can have are "submissive emotional/psychological trainwreck" or "hardened and unfeeling."

The Chozo all suffered from a highly communicable Doom virus
That is to say, a virus that causes anyone infected by it to be completely and utterly doomed, which is why they're all either dead, MIA, or disembodied, and their friends the Luminoth, Bryyoans, and those robots they left at Elysium aren't much better. They gave Samus enough of vaccine to keep her alive, but she still spreads the virus, which is what happened to her squad from her early Federation days, Adam, The Infant Metroid...

The Baby Metroid in Super was about to become a queen
In Other M it says that the Queen fought in the ending was "unaltered" and that only certain Metroids can become Queens.

Which is kinda interesting considering what happens in fusion (I'm thinking the above WMG regarding Samus' sterility could be jossed...)
 * ...I just had an image of samus leading her newly-born children into battle. And I think I can speak for the Pirates and the corrupt members of the Federation when saying that a very hormonal, post-partum Samus in charge of an army of metroids of various sizes is the most horrifying thing in the universe (although for that to be playable, as an almost Overlord style affair or perhaps even an RTS...)

In Metroid V, computer!Adam will get an android body.
As of Other M, the existence of androids is canon. Given how many ships Samus has gotten blown up or otherwise damaged/destroyed, she might look into some way to get Adam out of the gunship's computer so she doesn't lose him for a second time.

Phantoon .
In
 * This is supported by the fact that the series of minibosses that you fight before entering chamber are all warped in via portals identical to the ones he uses to summon his Rage Hands during the battle. Clearly, he had taken over in the time between Samus' departure and return. As for his physical absence during the main conflict on the Bottle Ship, it seems like his ability to warp in and out of local timespace makes it quite likely that he simply disappeared for a while, probably under MB's aforementioned orders to back off.

Sylux is .
Perhaps that is the real reason that Sylux hates both Samus and the Galactic Federation so much? He blames them for.
 * Damn, that's pretty deep. And heartbreaking.
 * You got your Event Horizon in my Metroid.

Phantoon didn't die in Super Metroid.
You only see it disappear. It probably left the space pirates and went to recover from its injuries, where it eventually

Samus is left-handed.
Not sure how wild a guess this is. You could make a case either way, but I'd say she's a lefty who trained herself how to shoot with her off hand due to the way the Suit works - with her off hand firing the weapon, she can use her dominant hand for more precise tasks like typing and so on.
 * Samus is always seen gripping her cannon arm with her left while aiming and as none of the weapons seem to have any recoil this seems to be correct.
 * On the other hand she could just use her left hand as a support for the arm cannon to increase stability, in this case she'd be right handed. Though considering how much she uses both arms for various tasks I'd go with ambidexterous, either naturally or through training.
 * I always assumed that she was holding it with both hands to make it easier to hold stable (even without recoil it's not easy to hold a weapon perfectly straight).

The Power Suit requires concentration to turn on and recharge but otherwise works normally.
There were Word of God statements around the time of Zero Mission's release about how Samus requires a massive amount of mental energy to activate, but never did anyone say concentration was needed to keep the suit on. Ever since Super Metroid her suit has automatically turned off whenever the sheilds are depleted, maybe whenever her suit deactivates, whatever the reason (the pirates in Zero Mission, The wall in Prime, the Ing in Prime 2,Ridley in Other M and Adam in Other M)is just completely beating the shit out of her, to the degree it depleted all of her energy.(At which point she would have to concentrate to turn the thing back on.)
 * Concentration being necessary to keep it on is evidenced by the suit's deactivation upon her seeing . Unless you think she and DECIDED to deactivate the suit.
 * Problem is, this violates things already established in the series, namely Metroid Prime 3 and Fusion, where the suit stayed on while she wasn't even conscious, much less concentrating. Hence the wild mass guess.
 * Original Poster, I never said anything about her deciding to turn the suit off, I mentioned that in all of the 2-D games since Super, her suit always turned off when energy reached zero, then resulting in game over. At no point is concentration indicated as required to keep the suit on, as during the Ridley scene he has his claw around her, is squeezing her, and hits her against the wall a few times, things that do damage, reduce the energy tanks to zero, and turn off the suit; like in SM, Fusion, ZM, and Other M itself. The suit doesn't turn off when she sees Ridley, it turns off after he grabs her.

The Metroid universe is the future of the Beyond Good and Evil universe.
The DomZ (BGE) have demonstrated the ability not only to steal "Life Energy" and perpetuate themselves using it, but to use that ability to create reconstructions of those whom they deplete--up to and including armor. They also seem to store their energy in the Pearls. Perhaps the "Pearls" are, in actuality, shell-like casings they build up in order to protect their true soft, inner forms--this is not unlike what some real-world creatures do, in particular, a sea organism called Syringammina fragilissima, a giant protozoan. Now, after the defeat of their Priest and loss of their primary life force source (I.E., Shauni), they lost the ability to maintain these bodies--but they could hold forms long enough to return to their home planet, not yet discovered by humans. There, they reverted to their true bodies--gelatinous, levitating creatures--and their old way of feeding, directly consuming genetic material and life from their hosts as parasites.

Meanwhile, the threat of the Alpha Sections gone, the IRIS network turned to a new social conflict: Fantastic Racism in certain portions of the galaxy between Humans and Hybrids. Sadly, they could not stop it. But IRIS was able to help certain groups of Hybrids escape, and Jade loaned them a portion of her powers to help protect them until they could restablish new communities in secluded portions of the universe. The bird-based Hybrids went in one direction, the reptillian hybrids in another, the moth-based ones still another, etc. The different populations each used the gift in different ways. The bird-peoples used it to help them make their chosen world livable for them--but it was still too harsh for most unaltered humans. They began to call themselves the Chosen. In their spare time, they started tinkering with some leftover Alpha and Hillyan armor they had lying around, and built much improved, full-body Powered Armor they could use to defend themselves with.

The reptillian people did much the same, making a harsh planet safe for them alone, but unlike the Chosen, who were happy to live unnoticed, they vowed revenge on the humans and started building up vast stockpile of weapons. They couldn't figure out a use for their gift initially (which Jade was really starting to regret giving them), so they just sort of left it lying around. It wasn't until a group of scientists--geneticially tinkering with a relatively benign pterodactyl-like creature they found one a planet somewhere--took a look at said creature's potentially fierce physical body and realized that the only thing stopping it from becoming, well, unstoppable was a killer instict and a way to keep on going even if it got knocked down. So they invested the Shauni power into the creature and trained it, tweaking its brain to making it intelligent, and continuously growing (so long as its life energy was fed). The result: A nearly-unstoppable killing monstrosity with the ability to regenerate from almost anything, not to mention a vicious inner energy. However, like the original DomZ, he needed to feed on flesh in order to keep his inner power source running. They dubbed it Ridley.

Meanwhile, time had corrupted the name of the avian people into "Chozo," and they were out roaming the cosmos one day (as you do) when they stumbled upon the homeworld of the DomZ. Knowledge of their kind had long ago passed out of Chozo culture, and anyway, there was no one left alive who would have seen them in their original state. They called them the "X", because they had no idea what these strange parasites were--but when one of them suddenly attacked, the life-moving power was frightfully reminescent to them of the darker side of the Gift. They still knew the Gift existed, but they had not done anything with it in a long while. Now, their culture had a legend about how a creature with the power to consume life had been defeated by a warrior who was a limitless fountain of it. Their Gift was supposedly from that warrior, so they decided to use the last of it and incorporate it into a warrior to drive aside the X. Unfortunately, removed from the heart of that warrior, the creature, driven by that life power, was as thirsty and bottomless as the X itself--it destroyed them, but anything else it happened upon as well. Reluctant to have used up their culture's treasured Gift, they abandoned the Metroids and X to one another. Until, of course, the former reptillians--now the Space Pirates--happened upon them...

Luckily, there were those around who knew what the X truly were and what fueled the Metroids. The IRIS network still exists--in particular, because the original members are still alive, rendered immortal by the powers of Shauni. They've pushed and manipulated things behind the scenes for a while, such as helping build the DomZ Sarcophagus-inspired stasis pods for the former moth people (now the Luminoth), but they resisted temptation to directly meddle until it looked like the DomZ/X might break out into the universe again. (Well, OK, they tried to put a stop to Ridley too, but he seemed to be "another Shauni" in that not even Jade seemed able to stop him from regenerating eventually.) Then, they began to work together to create one more Gift--the power to create one more Shauni. One of them, posing as a scientists, posed the idea of the Metroid vaccine for the X--which they imbued with the last Gift. More than part-Metroid, Samus Aran became a new Shauni--ready to take up the mantle in the fight against the DomZ-X.

Oh, and we feel like we should mention--there was one more group of Hybrids that got a Gift. Not only were they eventually vengeful, but greedy too. They tried to use the powers of the Gift to farm Pearls. However, the Gift and the DomZ-traces mingled with the pearls, and created a horrible, spreading crystalline virus. Not only did it destroy them, but the stuff kept growing and spreading until it penetrated the very heart of their planet. Nobody heard from them for centuries, until the thing known as Phazon started cropping up all over the galaxy...

The Metroid universe is the future of the Starcraft universe.

 * The founders of the Galactic Federation are the Terrans and the Protoss: Following the defeat of the Zerg at the conclusion of the Koprulu Wars, the remaining Terrans and unified Protoss form a formal alliance known as the “Koprulu Accords”. Eventually their combined technological prowess and resourcefulness allows them to extend their influence to the rest of the Milky Way galaxy, encompassing the Sol System, the former Chozo worlds, and annexes many other advanced worlds in the galaxy. The final product of this union and subsequent expansion is the Galactic Federation: a civil union of space-faring civilizations to prevent the horrors of the Koprulu Wars from ever happening again. As the centuries go by, the Koprulu Wars and the Zerg are forgotten, and the Xel’Naga is eclipsed by the mysteries of the Chozo. Phazon was also an attempt at discovering an alternative to the rapidly depleting vespene gas, but was determined too volatile for profitable use. The Space Pirates disagree. Eventually, one of the more prominent Chozo worlds, “Zebes”, is colonized by a science/mining team to uncover more Chozo artifacts. The Space Pirates are just as interested in the artifacts, and less interested in sharing. As a side note: Federation Marine power-suits look like bulkier, advanced Ghost and Spectre suits (possibly modified with Protoss technology) and Armstrong Houston’s (Houston Barrimonde in some media) power suit is remarkably similar to a modified Terran Marine armor.
 * The Metroid are the last remnant of the Zerg: The Zerg was systematically destroyed following the death of their Queen and the irreversible destruction of their Cerebrates; they began to devour one another, until only one species strong enough to survive remained. In an act of self-preservation, they sought out a world to gestate and evolve without the threat of destruction. The last overlords and overseers carrying the DNA of this infant species found a distant planet with a rich eco-system and a small enclave of Chozo. The Chozo recognized this species as the creations of the Xel’Naga, and quickly abandoned the planet to the alien invaders. The species of Zerg found the planet to be a perfect breeding ground for their further development and used the ensuing centuries to grow and prosper. They developed a method of energy absorption that was at least ten times more efficient than standard metabolic processes and allowed them to become the dominant life form on the planet. The planet: SR-388. Their ability to alter their genetic code as they mature (alpha, gamma, omega, etc.) and their susceptibility to Phazon and other forms of radiation is a genetic artifact of the hyper-evolutionary virus that originally spawned their forerunners.
 * The Chozo and The Xel’Naga are philosophical off-shoots of the same civilization, if not the same species: The Chozo and the Xel’Naga are both highly advanced species, technologically and biologically speaking. It is not unfounded to speculate that they may have developed as civilizations simultaneously. Furthermore, they may have developed on the same home world, as two sapient races sharing the same planet. They may even be the same species, the Xel’Naga having become obsessed with a sort of “transchozoism”, seeking to modify their basic biological structure through technology, psionic manipulation, and genetic experimentation. The Chozo proper may have seen such technological modification to be reckless, and sought to develop them-selves naturally, combining their technology with the organic processes of their environments and developing their psionic abilities slowly and deliberately. Eventually, the Xel’Naga left their planet after some unforgivable schism rent their relations with their planetary cousins, forcing them to wander the universe in their world-ships, continuing their experiments they started on the Chozo home world (foreshadowing the conflict between the Dark Templar and Aiur Protoss). History would show that they would end up destroying themselves with their own creations, the Protoss and the Zerg, becoming a dark shadow of their former selves. The Chozo on the other hand, would continue to colonize world after world, careful to avoid contact with either the Protoss or the Zerg (possibly through the same ways they repelled any Xel’Naga influence), until they too disappeared under mysterious circumstances. (Possible Ing persecution, Metroid (read Zerg) taint, or Phazon corruption? Or a shadow war with some remnant of the Xel'Naga?) On a similar note, Samus' Morph Ball technique works by temporarily shifting her physical body into a psionic warp-space pocket, similar to what the Protoss use. It makes sense that an equally advanced species such as the Chozo would have similar technology. Her suit then compresses itself into a ball, which Samus controls psychically from the warp-pocket, and explains how she can see where she is going.
 * Ridley’s resurrections are similar in origin to the Cerebrates’ psionic resurrection: The Space Pirates are obsessed with Zerg bio-physiology (see below). They constantly strive to make themselves greater and greater, equally obsessed with the concept of “Purity of Essence and Form.” They continuously modify themselves with ancient technologies and strange xeno-biological processes. Ridley is the culmination of psycho-biological experimentation and meta-cybernetic development. He is essentially a being of pure psionic energy, able to restructure himself as he was from a kind of proto-genetic soup the Pirates manufacture just for him, or implant his psyche into cybernetic duplications of himself. He is essentially a Cerebrate without the need of an Overmind (But see below). (Kraid is a similar subject, but is more of a straight cloning procedure rather than the kind of psychically transcendent being that is Ridley.)
 * The X-Parasite is a semi-sentient, self-sufficient descendant of the original Zerg hyper-evolutionary virus: On SR-388, the last Zerg remnant, called “Metroid” by the Chozo enclave stationed there, continued to develop itself using an evolved form of energy absorption and the hyper-evolutionary virus that spawned them. With time, it became the dominant life-form on the planet and as a side-effect, spread its genetic influence throughout the planet’s eco-system. The Zerg hyper-evolutionary virus therefore integrated itself within the biospheres of the planet, eventually manifesting itself as an autonomous life form. The Metroid kept the life form, eventually referred to as the “X-Parasite” by Federation scientists, in check, but when Samus Aran destroyed the Metroids on the planet, the virus was able to further develop itself, becoming the lethal threat encountered in “Fusion”.
 * The Space Pirates are a group of descendant Protoss fanatics dedicated to combining Zerg biology and Protoss technology, hence their obsession with Metroids (all that’s left of the Zerg) and their predilection for Chozo (read Xel’Naga and therefore Protoss forerunner) technology; this cements their desire to become “perfect” and the most dominant species in the galaxy: “Purity of Essence and Form”. As such…
 * Mother Brain is an attempt at recreating the Overmind: As noted, the Space Pirates are a group of Protoss descendants shameful of their species' integration into the Galactic Federation. They have researched extensively the records of both ancient Xel’Naga and Chozo technology and development, and have come to the conclusion that the Xel’Naga were extremely close to achieving their goal of the “Perfect Life Form”. They then begun to aggressively acquire Xel’Naga and Chozo artifacts to solidify their research, and begin development where the Xel’Naga left off. Such developments are: The Metroids as a weapon; Ridley’s resurrection abilities; their marked differences in appearances amongst each-other and from the original Protoss; and finally, Mother Brain. In their attempt to emulate “Purity of Essence” they sought to unite themselves in the same glorious hive-mind the nearly unstoppable Zerg once had almost a millennia earlier. Through countless experiments and development, they created the first Overmind prototype: Codenamed – Mother Brain. Their experiments finally giving fruit at their research installation on Zebes, they initially used Mother Brain as a massive DNA computing processor to accelerate their research. Unfortunately for them, they did not count on the bounty hunter Samus Aran to destroy the Mother Brain and the Zebes installation. They would later re-inhabit the facility in an attempt at modifying the hyper-evolutionary virus found within the last-surviving Metroid to resurrect the Mother Brain, as well as give it a greater defensive capability. To no avail, however.

Phantoon feeds off of the souls of the dead.
Look at all the death that occured on the Bottle Ship. . That would explain why he's so gigantic and has more ghostly attacks than before. The Bottle Ship has drawn him like a fly to honey. Also, in the Wrecked Ship, he had access to much less life force to devour, and as such was smaller and weaker, as well as less tangible.

The entire Mother Brain battle in Super Metroid was a hallucination.
After being attacked by the Super Metroid, Samus was put in a high-adrenaline near-death experience and her mind didn't understand was what going on. After defeating the Mother Brain in the jar(the only real form of mother brain), the Super Metroid returns and consumes the rest of the Mother Brain's energy and evolves in an Omega Metroid that Samus believed was Mother Brain. The "dinosaur" Mother Brain isn't very different from the shape of the Metroid.

Samus has dual personalities.
Inside the power suit, she's tough, brave, emotionless, intimidating. Statuesque, as put by Moviebob. But outside the suit, she's scared, dependent, and rather clingy. This lesser personality breaks through every so often if something rattles Suit!Samus badly enough. It kind of evokes a bit of Fridge Brilliance when Super Smash Bros Brawl made Samus's power suited and zero suited selves seperate characters...

Samus didn't suffer from character derailment in Other M
Samus has always been a delicate flower who wants a big strong man to protect her, but she wants to make sure that man will be up to the job. Proof? She only gets out of her suit and shows some fanservice if you beat the game really fast or get all the power ups, thus you have proven you are capable to be with her! Adam is simply the only non player who has accomplished such a feat. This of course assumes Samus can ignore the fourth wall, but Fan Dumb people like me just really need a good excuse to stomach how she was portrayed in that game...
 * So Samus is a Best Her to Bed Her type? That's... actually not so difficult to stomach.

Metroid V will use a 2.5D engine ala Fusion's, and blend Other M's cinematic approach with the older game's exploration
That way, everyone's happy. The people who want to see more cinematic from Metroid, and those who still want the open exploration. Plus, the 2D games sold much better than Other M, so they probably are gonna make it a 2D game rather than re-use Other M's engine.
 * Confirmed. Look up "Metroid Dread". Then come back here, and give up all the hope you just built up, because it's still a LONG ways away.

The ship seen in the Prime 3 100% ending is Dark Samus
Every 100% ending involves Dark Samus in a way(In Metroid Prime's 100% ending, Metroid Prime was revived as Dark Samus. In Metroid Prime 2, it has Dark Samus reforming), so Prime 3's ending clearly involves Dark Samus (Now known as Dark Gunship) being revived as a space ship and going after Samus for revenge.

The power suit runs on life energy, or alternatively can harness any type of energy like the Metroids

 * That's why you get energy for your suit from enemies.

Crocomire in Zero Mission...
See, in this spritesheet for Zero Mission, Crocomire's skin is fit together and is a dark reddish grey. In Super Metroid's sprite, however, his skin is a bright red and appears to be dripping. This implies that Super wasn't the first time he was pushed into lava. How he escapes is up to anybody's guess. Perhaps he pulled that last stunt he did in Super that ultimately fried him to the bone, but didn't try to initiate a part 2 of the fight.
 * ...Was obviously meant to survive the battle, but not without a fair share of permanent injuries.

Samus's Character Derailment in Other M was an extended high-functioning Heroic BSOD.

 * Samus isn't a fragile flower or dependent on others most of the time, but Other M picks up right after Samus has taken a real emotional sledgehammer blow when the baby Metroid sacrificed itself for her. The reason Samus seems to lack her independent spirit and stoicism implied by the other games is that she's hit an emotional nadir from losing the only "family" she had for the third time in a row, only now she's not only lost her biological parents and the Chozo, but the closest thing she's ever likely to have to a child. Under that level of depression, she's still able to function but everything about her is just phoning it in; she's lost the ability to muster initiative and operate alone and unsupported like normal, and she tries to deal with it by trying to surround herself with people, like Adam, and to get along with the one remaining parental figure she has left even though Adam's orders restrict her ability to get things done. The depression only deepens when Ridley revives; Samus had been sure this time she was finally rid of him forever, but now she sees that she can't seem to keep anyone she cares about from dying while the monster that ate her parents won't stay dead no matter what she does. Hence, freezing up and needing help. In the next Metroid game, she will be able to overcome the depression and undergo Character Rerailment.
 * This is certainly plausible, seeing as Samus does show a number of textbook signs of Post-Traumatic Stress Disorder in the game. She may have this Character Rerailment in Metroid Fusion, during which she shows signs of being a Death Seeker and slightly unhinged before rising to the occasion and completing her rogue mission at the end with renewed resolve to stay alive.

Samus's original suit was restored at the end of Metroid Fusion.
When Samus absorbs the core x of the SA-X at the end of the game, her fusion suit takes on a palette similar to her old armor, and she gains the ice beam ability. The game's staff wanted to show her actually regaining her old appearance, but technical limitations prevented them from swapping her sprites with that of an SA-X. After all, the implications that Samus has somehow "conquered" this alternate appearance are pretty strong: Fusion suit has similar colors to her old armor, and she can use the ice beam. In the end, they just went with the palette swap and re-used a colorswappable image of her in the ending cutscene, for consistency's sake. However, if the theory was true, it would put quite a different spin on the final battle.

Omega Ridley is not actually Ridley
He is actually the equivalent of Dark Samus: Meta Ridley's Phazon (and possibly mechanical) shell having been separated from him and gaining sentinency. That explains why he explodes at the end of the battle.

== Samus Aran is the Audie Murphy of her time and the Metroid series is a collection of episodic biopics more or less faithful to the memoir she wrote after retiring. ==

After a successful career as a bounty-hunter/soldier/planet-destroyer/nightmarish-personification-of-retribution, a retired Samus Aran decide to write her memoir. The memoir is an instant hit, and eventually someone buys the rights to adapt her book. Except that:
 * In the future, video games have completely taken over the silver screen, so instead of a biographical film, we have a biographical game.
 * So much happened in her life and her memoir is such a doorstoper that a single game would be overwhelming.

So in the end a whole series of biogames is commissioned:


 * The first episodes are made under the careful watch of a classical director and maintain a somewhat conservative approach of describing the events and only the events: those are the first three 2D Metroid games.
 * Said director die in a tragic spaceship accident near a chronically overcrowded hypespace crossing.
 * Eventually, the adaptation is given to a young team of ambitious yet nerdy developers from another planet. Turns out that Samus was a very knowledgeable badass (being raised by Sufficiently Advanced Aliens can do that) and included tons of footnotes in her memoir. Trying to do justice to that, the new team includes them in their games in the form of the scanning ability (hacking into the Space-pirates' computers was never a gimmick of Samus' armor; she was just that good).
 * Fearing that the critically acclaimed approach of the second team of developers might grow stale, the studio which holds the rights to the adaptation decides to choose a third team. This team decides that the first approach (only the events) too dry and the second one (footnotes, footnotes, footnotes) too nerdy. Plus, a lot of her memoir includes the now old and retired Ms. Aran doing a lot of introspection about her past deeds, introspection which was never at the core of the previous episodes of the biogame. The third team decides then to put a bigger emphasis on it, except that it turns out that the audience was not that interested about the doubts and questions of a Retired Badass and wanted to see more of her numerous impressive feats of badassery. The last episode is very heavily criticized, making some people wonder if the last installment has put the project of adapting her complete memoir in jeopardy.

World Building
The reason behind why no games take place after Fusion. They are world building by establishing the Galactic Federation and cementing canon. Most likely any game after Fusion will most likely have the Federation be the villains. In order to tell a better story it became necessary to show how Samus interacted with Federation in the past. This way we can see the corruption of the Federation. In Prime 1, mostly showed a typical mission that Samus would take. Prime 2 shows us a bit more about the Federation through the Marines. The Marines are good soldiers and you can relate to their terrible fates. Prime 3 showed what it would look like if Samus worked perfectly with the Federation. Gives us a deeper look into the Federation and makes us like them, but at the same time a little bit of corruption can be seen. The Federation decided to use Phazon as a weapon despite being a very dangerous resource. The Aurora Units are introduced and seem to parallel Mother Brain a lot. Now Other M, foreshadows (or references) the events in Fusion. Showing how the Federation can cause problems with Samus and how it treats its soldiers as pawns. All this is building us up to an eventual sequel.

Nintendo either mistranslated or misunderstood the definition of "bounty hunter"
Let's face it, folks, Samus is no bounty hunter. She's a mercenary. She is always working for corporations and never once is she working entirely by herself to hunt down criminals. Hell, her bounty hunting career is almost never even mentioned in the series. Yoshio Sakamoto probably mistook "bounty hunter" for "mercenary".
 * She's collecting bounties on entities labelled threats and taking commisions for specific missions. Mercenaries tend to be commanded like any other troops when you pay them.
 * This seems likely when you learn Nintendo really didn't like Retro's initial plans to have Samus be actively bounty hunting in Metroid Prime 3, which lead to Retro calling her a "pro bono hunter". The question becomes then, why did it take them so long to catch on and why haven't they tried to correct the "misunderstanding"?

Each and every nucleus in a cell from Ridley's body functions as a black box
Other M is a real discussion starter and there have been several speculations about whether or not Ridley has genetic memory. Well I think that his cells store some information about the most dangerous thing he's ever met. The information would be such things as what the thing, whether it's a predator or a sheet, looks like as well as how they're dangerous to him and what stage of the life cycle he was in when this threat was encountered. This would serve a very good purpose when breeding. This is because the data would probably be in the offspring's memory and make the newly born "Little Birdie" able to know about some things that it shouldn't even try to engage until it has the abilities requred to stand a chance against the threat in question. This also means that if you clone an individual by putting the nucleus from one of it's cells by transplanting it to an ovum of the same species or a species with almost the same cell structure this black box info would still be there. It goes without saying that the same thing occurs if you use the slightly cooler cloning method of simply making cells massproduce and recreate the individual that way.

This explains why the "Little Birdie" encountered in Other M doesn't just attack Samus on sight, it knows that it'd get shot to bits as the source of his information was mature and still lost. When he reaches his second stage of the life-cycle he sees an excellent chance at disposing of Samus by pittinging monsters on her much weaker allies and forcing her to come out followed by pinning her to the ground and try to stab her with his tail. Then when Anthony fires off his Plasma Gun he gets registered as the new biggest threat to Ridley's existence because he had Samus more or less at his mercy. This is why he doesn't just kill Samus immediatly when he's encountered in his adult form. So why did he attack samus first then? Well he doesn't know that the GF-trooper with her is Anthony yet and he hasn't really done anything threatening yet. But when he shoots Ridley again he realizes that the yelling GF-trooper isn't yelling because he's afraid of him, but instead yelling because he wants to fight and kill Ridley and therefore it must be his largest threat that's back. So once Ridley is back on his feet he immediatly goes for Anthony who's a bigger threat than Samus now. When Anthony is defeated and probably not coming back he sets his focus on Samus yet again and soon realizes that Anthony couldn't hold a candle to her when she fights Ridley in more even circumstances so he flees. He does this in order to preserve his own existence and maybe get to try and rid himself of his biggest threat once more or just escape from it altogether. Then he meets and automatically gets imprinted in the black box as the biggest threat because it actually killed him. Then when he gets infected by the X-parasites in Fusion the X get to know that the biggest threat that this life-form has encountered is and that the person with a red helmet and greenish arm cannon is really dangerous as well. This gets taken even further in this game as Samus has Metroid DNA in her now and that DNA happens to be the DNA of so a she's basically two threats in one and gets highest priority on Ridley X's kill list.

Samus' BSOD in Other M wasn't the first, it was the worst
According to Sakamoto, the Other M Samus is the canonical one. That would imply that she has a meltdown every time she sees Ridley, we're just too far removed to see it (Kinda like Ciaphas Cain; everyone thinks that noise he's making is a Battle Cry, when it's actually him doing a really good job of disguising a Girly Scream). Other M was the first time she has a voice actor. How do we know she isn't hissing obcenities through her teeth whenever she's fighting him? Her freezeup wasn't "Oh God, it's him!", it was "Oh, God, He's never going to stay dead!" She's fought him almost twice per game so far (give or take a game or so)? She probably had nightmares about him for weeks afterwards, each and every time. These little cracks finally spilt out when she met him yet again on Bottle Ship. She failed her SAN check due to being so emotionally vulneable and stressed out. She didn't lose it in Fusion because she knew that Ridley was a clone/ zombie, and by absorbing the Core X mimicking him, it would be like taking a big fat bite out of his heart so she's finally rid of the fucker. Sort of a "last Hurrah!" deal.

Phantoon is Mantorok
And the Arans were related to the Roivas'. As the last surviving Roivas decendant, Mantorok needs Samus to free him so he can take over the universe (don't ask me how he got sealed away again). By attacking her in places where the veil of reality has been thinned by suffering and death a certain number of times, he's manipulating her into doing this. This also provides an explanation for Skeleton Crocomere, it's really a Mantorok Zombie. In V, he will attack her one last time and win. Forver.

Related to the above, Sylux is Pious Augustus
He is attacking Samus so she never beats Mantorok/ Phantoon enough to free him. The armor has been blessed by all three ancients, who managed to put aside their differences for once, hence the purple and green color scheme. He uses the Shock Coil to save on magick.

Samus killed 9 SA-X's, and the metroids ate the 10th
The SA-X cloned the genetic data on her upgrades and split off core-X containing them to infect the boss monsters. Adam misidentified them as pure SA-X clones. One was specifically made to infiltrate the Metroid lab.

Other M will be subjected to various Take Thats in the next game, establishing it as Broad Strokes
My bets are
 * Federation propaganda that assures citizens the space pirates are mindless and can't think of anything clever, then go on to talk about the revolutionary new technology that has been seized from them.
 * A Pirate Log that claims Aran fears General Ridley, then either gets punished for his stupidity, or has others mock him.

Samus has autism.

 * It's the reason she works alone as a bounty hunter on often deserted planets, rarely speaks (exept to herself), lacks well-developed social skills, remains unwedded (lets's be honest, she could have ANYONE she wanted), works under her own volition, possesses lighting-fast thinking, calculating, and problem-solving skills, and remains calm even in highly-strenuous situations (eg: having little trouble taking down Ridley while falling down a reactor). Then again, this may not be the case because of, well, you know.
 * If not by nature, then she's certainly autisticish by nurture. Being raised by a bunch of aging 500-pound canaries seems counterproductive to learning how to deal with other humans. (And hell, that breakdown could have been compounded with sonic frenzy ability - sensory overload heightens emotions, and heightened emotions make it difficult to process all the sensory input.)

Samus had depression as a child.

 * Duh. But also, pay attention to her end game outfits. As the technology's grown to show her arms in clearer definition, she's taken to covering her wrists. Even in flashbacks to the age of ten or thereabouts.

Metroid takes place in the cthulhu mythos.

 * there are many things to point out, first off the Luminoth are the Yaddith, the beings from yaddith are described as creatures with similarities to mammals and insects that are described as "snouted" their original homeworld was destroyed so they must wander the universe, They did so in "light beam envelopes" similer to the technology used by samus with the light suit to travel later in the game. Additionally the Ing may be the dark young of shubb-niggurath

The Wii U Metroid game will be simultaneously first-person and third-person.
The television screen could show Samus from a third-person perspective where she can run around and jump in a manner similar to the 2D games and Other M. Meanwhile, the controller will show Samus in a first-person perspective akin to Metroid Prime, where the aiming is done by means of the controller's motion controls. Thus, the main screen would be used for exploration, while the controller's screen would be used for combat.

Extrapolating further, let's say you have one of those "Finishing Blow" maneuvers from Other M. You could jump on top of the enemy and then, while up there, aim at specific weak spots around it's head and/or body. This could be helped by a Camera Lock On akin to Metroid Prime 3: Corruption, in that Samus can strafe around the enemy while still maintaining free aiming. Furthermore, the controller's screen could be used for different visors while keeping the main screen looking normal, in order to keep a consistently immersive feel.

Samus's Heroic BSoD in Other M is justified, because Ridley was only ever vaporized once.
The justification is based on a number of sub-WMGs. First of all, integrating mechanical components into dead bodies to return them to life is a common occurrence in the Metroid universe, or at least the Space Pirate empire and Samus knows it. It's already been done at least once with Mother Brain. Second, despite Ridley's body apparently vaporizing when Samus defeats it in the original Metroid game, that is not the case, only doing so due to graphical capabilities. Ridley's body survived, and was eventually recovered by Space Pirates following the conclusion of the first game, eventually integrating the mechanical parts that would turn it into Meta Ridley. Notice that whenever the games had the graphical abilities, Ridley was never shown completely blowing up. In Metroid Prime and Metroid Prime 3, your victory caused parts of it to start bursting, but the last we see of Ridley each time you beat it is the dragon falling off screen.

These allow for two things. First of all, every time Ridley was defeated between Metroid and Metroid Prime 3, its body was never fully destroyed, and Samus knew it would eventually be rebuilt, not being surprised upon facing Ridley in the next game. Second of all, that means Ridley only ever truly died once: when his body was vaporized in the Zebes destruction at the end of Super Metroid, the only time Ridley is ever caught in a massive explosion that vaporizes all it touches. This is why Samus went crazy upon seeing a revived Ridley in Other M. While every other time she killed Ridley, she knew he'd come back, his death in Super Metroid was the first time she truly believed he could never come back, since the planetary destruction vaporized his body. Thus, when he appeared in the Bottle Ship, she freaked out, believing there was no possible way he could come back to life after what happened following their last face-off.

Guys, don't panic. This may sound crazy, but I think Samus Is a Girl
Think about it. It just seems to make sense. The long hair, the feminine name, the female voice actor, the boobs. It really kinda makes sense if you think about it.

The next game will force Samus to face her worst nightmares...
...as in Metroid's hardest and most terrifying bosses. Most likely would be an attempt by Ridley to cause her to go into a total mental breakdown, which would make it easy to finish her off. The bosses fought would be these(though not necessarily in this order): Nightmare, Phantoon(Other M), Meta Ridley, Mother Brain, and Kraid. Plus a potential new foe.

Samus is NOT a girl!

 * Samus was raised as a girl, but in fact is not. She thinks she is, dresses like it, acts like it, and so on, but she is not technically a girl or at least was not born female. Samus was either told by her parents that she was a girl, or she (for some inexplicable reason) began to think she was after the raid on K-2L and her adoption by the Chozo. So as to not heap further psychological trauma upon Samus by revealing the truth to her or having her learn it on her own, the Chozo surgically altered her appearance (and perhaps her genetics) to be female after the raid on K-2L. For all intents and purposes Samus is a female now, but she was not one to begin with.
 * Alternatively, Samus is a man in drag who gets off on pretending to be a woman. And everything in Other M and Fusion isn't canon. Neither is the manga. Unless it is? Because why not.

Ridley has a terrifying fear of the number '2'.

 * He appears in neither Metroid 2 or Metroid Prime 2.

The Chozo and the Galactic Federation are the true villains of the series. The space pirates and Ridley never actually attacked K2-L.
Think about it. The ONLY time we ever know of the space pirates attacking innocents is during Samus' extremely early childhood, which just so happens to be right before she gets implanted with Chozo DNA. What else could they have changed during that time frame? Throughout the rest of the series, they(The space pirates) only attack the Galactic Federation or the Chozo, a race that's responsible for just about everything bad that happens in the Metroid series. Creation of Metroids, a DIFFERENT assimilating monstrosity that could annihilate the universe, instead of just outright annihilating the X? Check. Metroids responsible for the creation of phazon, yet ANOTHER weapon of mass annihilation, which also happened to create Dark Aether for yet another race of xenocidal Eldritch Abominations? Double check. Creation of Samus Aran, who brings nothing but death and destruction wherever she goes? Triple check.
 * The Space Pirates are said to attack everyone (hell, you can read their own logs about looking for new targets). The Chozo only created the Metroids (and possibly Mother Brain, but that's left ambiguous and it's just AI Is a Crapshoot anyway). Phazon wasn't created by the Metroid Prime (the Metroid Prime was just mutated by it) and the only influence the Chozo had on Aether was apparently making friends with the Lunimoph. Also Samus is theoretically no more powerful than a normal Chozo warrior (it's just that some adopted human happened to be the only one who chose to become one), incidentally Aether was pretty free of death and destruction when she left it.
 * She nearly whipped out the Ing and destroyed their planet leaving Aether, but they kind of asked for it.
 * I didn't say "The Metroid Prime" created phazon, pal. Didn't you notice the MULTIPLE Metroid Prime shells on Phaaze? It's a big hint towards the "Defective Metroids were the initial source of Phazon" theory. I'd like to know which logs you refer to, by the way. I specifically referred to indirect destruction of the Luminoth. It was a leviathan that created Dark Aether, remember? Aether was left in the hands of a sect of hypocritical genocidal space-moths, or do you think every temple filled with death and destruction wasn't around before the Ing showed up?

Fusion-Ridley was just a member of Ridley's species, not Ridley himself.
Ridley isn't the only member of his species - just one of the more infamous. The corpse seen in Fusion was a researcher who died some time before the start of Fusion, and his body was iced in preparation to send back to his homeworld. This also explains Samus' complete non-reaction to him.

Dark Samus will impersonate Samus after Fusion.
Bear with me. Samus has gone rogue having defied the Galactic Fedaration. Dark Samus' demise is questionable at best. Dark Samus has been laying low, gathering her strength, and spotting weakness, makes her return and begins working for the GF claiming to be the real Samus, while Samus now stuck in her Fusion suit doesn't even look the part and is conveniently an enemy of the state. Considering Samus is now part Metroid she'd even fail a DNA test in any attempt to prove she's the genuine article.

Eggplant Wizards will get Metroid game equivalents in the future?
Because they'd be even worse in an open ended game that is easy to get lost in.