Mega Man X/WMG

Mega Man X is Domon Kasshu.
This should explain it all.
 * This also explains how he could use Hadouken and Shoryuken - moves not so extreme compared to the rest of The School of The Undefeated of the East.

Power and Speed "RP" Rating
A reploid's Power and Speed are measured in an odd, unexplained unit called "RP." Say that "RP" stands for "Reactor Power," and the two scores added together add up to a reploid's maximum energy output, labeled "Reactor Output." For example, in X3, Vile's Power score is 9200, and his Speed score is 7200. If his Reactor Power (RP) scores are added together, he has a maximum Reactor Output (RO) rating of 16400. The reploid's RO rating would be a general indication of their strength. A reploid like Crystal Snail would be very weak, with a RO rating of only 7300, while a more powerful reploid like Bit has an RO rating of 27400. Seeing as X was meant to have limitless potential, his RO rating is unmeasurable, leading to the "????" score he gets for Power and Speed.

Person(s) responsible for creation of "Day of Sigma" are huge fans of G Gundam US dub.
See above. And Sigma is Master Asia too.
 * Sort of true: they're Ocean Studios, the peeps who dubbed G Gundam in the first place.
 * X8, Command Mission, and Maverick Hunter X overall were dubbed by the Ocean group.

It was supposed to be Wily that repaired X in the end of X5
In Inafune's original plan where X5 was the finale, Wily repaired X, uploading corrupted data into him, thereby making him go nuts by Mega Man Zero.
 * Except that it was always meant to be Copy X in MMZ, even before the retcons.
 * Except that X is the original villain in Zero. The retcon and Continuity Snarls was what led to the creation of Copy-X.
 * Oh, I don't think that was the original plan. I think Infaune originally planned for X to have a Heel Face Turn Face Heel Turn on his own accord, becoming more aggressive in order to deal with Mavericks. After all, the Zero Virus normally drives you Ax Crazy instead of making you become a Knight Templar/Well-Intentioned Extremist (Sigma managed to resist for some time because of his specs, but became corrupted because Death Is Cheap).

The main reason why X decided to stop fighting in the seventh game.

 * The main reason he chose to "retire" is not because of the unscrupulous methods of handling the Maverick problem. The real reason was because a new character was going to be in the game, and Zero already steals enough screen time from X, so he decided to just call it quits. He realized Axl isn't all that likable in the game, so he came back.
 * Or the fact that fighting Sigma just wasn't working? The only real way to stop the Maverick Virus was with a technical breakthrough: the wars were just buying time. Retiring from the hunters to work with a team researching his immunity makes perfect sense: it was Zero being sealed away to be researched to create the Mother Elf that defeated the virus in the original timeline, not Zero the hunter fighting Sigma. X was around when Dr. Cain was creating the first reploids, repairing irregulars, etc. Even ignoring the fact he's Dr. Light's heir, given Sigma's tendency to target scientists (or they get themselves infected while trying to research a cure), his age, his experience with the virus... he's frankly wasted on the battlefield. If Zero was capable of holding the line and fending the Mavericks off, then it only makes sense for X to work on trying to solve the real problem. Of course, if one of them had to be taken off the battlefield, it would make more sense for Zero to turn himself in, reveal he's the source of the virus, and let them study him, but Capcom wanted more sequels...
 * Or perhaps he could leave so he could actually help repair human/reploid relations and actually make a society where they both live in peace? Even Zero admits that a fighter like him can't change the world, and instead fights for people who can actually change it legitimately. X is a smart, kind, compassionate reploid who's wasting those traits on the battlefield instead of the greater society, where his legacy as Light's last creation could do some good. To be honest, it slayed me that Capcom just had X just sitting out in X7, instead of going to reserve status and spending his time rebuilding the world after the Eurasia Incident. It could even lead up to his status of basically ruling Neo Arcadia in MMZ.

The Maverick/Zero Virus is based off the Evil Energy in Mega Man 8.
Think about it. When Bass used the evil energy, it gave him a bright purple aura and gave him a major power boost. When Zero turned Maverick in X5, he was surrounded in a bright purple aura that gave him a major power boost, as well as actually giving him energy. Although Wily lost the original source of the Evil Energy, he created a digital form of it and used it for the power-base of his greatest creation.
 * This article lends credibility to this idea, but with MM 10 it's too soon to say for sure.

X's design is was inspired by Duo.
Compared to Mega Man's design, X is far more advanced in both specs and abilities, to the point that he was super-advanced even a century in the future. Where did this major technological leap come from? The answer is when Doctor Light helped repair the highly-advanced alien robot Duo in 8. Although he wouldn't be able to understand everything, he understood enough to repair Duo with all his strength and powers. Doctor Light was heavily inspired by what he managed to reverse-engineer while repairing Duo and applied the same techological advances when creating X.
 * I'd be willing to say that the pinnacle of Light's Duo-Based technology was the Ultimate Armor. It certainly explains why its Giga Attack is the Nova Strike.

There is no Maverick Virus in Maverick Hunter X.
The Maverick Hunters act more like reploid police in MHX; conducting investigations, tracing hackers, doing raids on hide-outs, and so forth. The game intro even says that the Hunters were created to control illegal reploid activity, not berserk reploids. There's also the fact that every Maverick had an actual motivation to join Sigma, or made it clear that they were forced to do so. And finally Sigma, the big bad of the game, had a very concrete reason to go Maverick and never has his little "I'll be back" message after the credits. From the way the game is presented, you could take out the virus completely and nothing would change. Considering that the MHX series was supposed to how Inafune wanted to envision the series, and the virus revelation was only thrown in on the third game, it's possible that there's no virus in the game at all.
 * In essence, "Maverick" simply means a Reploid who doesn't fall into social norms for any reason ranging from Ax Crazy-ness to freedom fighters.
 * Exactly. (Or for being a criminal.)
 * This is the case even in the original X: Some reploids willingly rebel with Sigma, such as Chill Penguin and Armor Armadillo, but others, like Storm Eagle, have higher morals, and thus must be forcibly turned by the virus.
 * Another possibility is that Zero was never built by Dr. Wily in MHX; he's just a normal, albeit high-performance, Reploid.
 * Unlikely: MHX was meant to be a reboot closer to Inafune's vision. Zero being Wily's creation is a central part of the character.
 * Actually, the original plan was for Zero to stay dead, but he proved too popular to get rid of. There's also an interview with Inafune on 1-up.com I think, where he explains the original series was supposed to end on 6, with Dr. Wily in prison, but MMX 1 sold so well that Capcom decided to revive the original series. It's possible that Dr. Wily was retconned into Zero's creator just so he could stay relevant, add drama to the new story, etc.

The Maverick Virus was originally a lot more subtle.
As an alternative to the above. Dr. Wily was all about sabotaging Dr. Light's work. He'd already done the reprogramming thing in 1 and 9, taking over the Robot Masters who had certain hard-coded aspects to their personalities, both making them his own and making them look dangerous. But X and the Reploids? That would never do. They had complete freedom to grow and change psychologically based on their experiences and decisions. So, the virus he built into Zero was designed to subvert that, to find any motivation they might have for turning against humanity and amplify it, burning in the back of their minds, until they made the decision "freely". This only changes at the end of X2, when Sigma merges completely with the virus in himself, becoming first a free-floating precursor to the Cyber-Elves, then spreading as an "upgrade" to the virus when that is destroyed. His desire for followers causes it to act far more suddenly and dramatically from then on.
 * Perhaps it works as a tempter—it reasons with them why they should be a Maverick, and uses that to corrupt them. Sigma is the best example of this: when he first went Maverick, he was still as noble as he used to be, yet working as a Maverick. After gaining immortality from the virus, said virus slowly worked to rot all that he once stood for. His moments of being a Magnificent Bastard is due to him understanding the virus more and more.

X's true unlimited potential is that he can spontaneously evolve.
We already know that X can copy the abilities of others and constantly alter his own body/weapons to accomodate new weapons and armors. However, Maverick Hunter X heavily implies that X has a much greater potential than that—Doctor Light says he named X after the variable that symbolizes unlimited potential, to learn and grow far beyond his original specifications. MHX gives us the perfect example; X had been taken by surprise and critically injured by Sigma, had lost his buster arm, and was in serious danger of being killed. What did his systems do? Found an alternate solution. Faced with certain death, his systems spontaneously altered themselves so his other hand could become a weapon and then pushed itself into overdrive so he could overcome his damage long enough to fight back. Basically, X gained a new weapon on the spot without any outside data. The implications of this are huge—a robot that can constantly change and gain new abilities without any outside interference, a new independent being and the first of a true species.
 * Further note: This also explains why Sigma allows X to live—Sigma wants reploids to evolve beyond what humans created them for, and a reploid that can always evolve is a crucial tactical advantage. By forcing X to evolve, he proves that all reploids can change if the chips are down.
 * Further note #2: This could mean that X's hadoken could be more than just a silly easter egg. If his systems could turn his hand into a deadly weapon, forming a ball of energy between his palms is only a half-step away.
 * Further note #3: This also explains why X's base abilities keep changing between games, to the point the X Biometal in the ZX series comes with X2's double charge shot power. As he fights against worse and worse odds, his body adapts new powers, using the armors as a guide, to improve his odds of survival.

Zero failed at taking out the enemies in front of Sigma's fortress in X1 because the enemies respawned behind him.
Think about it. He says he's going to keep the defense force busy, and then two seconds later, you're fighting for your life against those goddamned turtles. It could be argued that he's taking on something worse, but he just went in that direction like five seconds ago! You'd think he would bother to take out the bloody things for the sake of X's sanity.

The Face Room boss from X1 is, in fact, the android recreation of Face, Nick Jr.'s old host.
WMG, destroying your childhood one day at a time.
 * Thanks, now I'm imagining Rangda Bangda saying "Welcome to Nick Jr! Doo doo DOOOOOOO!".

Repliforce was an attempt to create a loyal fighting force that backfired.
Now that the world knows of the Maverick Virus, the council wants to expand anti-Maverick measures to keep the peace. But many of the Mavericks from the previous three uprisings have been Hunters, and the council are worried about expanding a fighting force that have had so many defections. The answer? Make a new fighting army without such a problem. They create Repliforce instead, giving them flashy 'uniform' designs, a bold logo, and deeply-programmed beliefs in honor and warrior pride so they'd never betray their brethren. The council believes that this heavily unified and loyal group will be better at hunting Mavericks. Except that when the government accuse them of being Mavericks, the very design they were given caused them to over-react and rebel rather than allow their great name to be tarnished. Even those who were against the coup eventually gave in and followed them, just like Iris. The council's attempts to make a 'Maverick-proof' army instead made the very worst one to date. "Compensate for Sigma and Doppler program failures Uphold Reploid Sciences: Research & Development Maximize Reploid efficiency Increase troop response time for MH-v3 Prevent further Maverick action"
 * Uh...You do know that WMG is for Wild Mass Guessing and not things that are confirmed and stated outright in the game's instruction manual, right?
 * All we know is that Cain Labs made Repliforce and for some reason they had Honor Before Reason to the point of suicidal stupidity. I was trying to explain why they were so stubbornly loyal and why they were programmed that way beyond simply 'because we need an excuse for a game'. My X4 manual is buried deep in my garage, but I've checked the wikis and nothing there explains why they were fanatically loyal nutcases. There's a reason why people scratch their heads on why Colonel and the others were just so unreasonable and somewhat disturbingly cult-like (the salute, anyone?), even on this very wiki (see Just Bugs Me, What an Idiot!, etc). It might be just me, but I wanted to come up with an actual reason. Anyone get what I'm trying to say, here?
 * The manual does state that Repliforce was made in response to the amount of Maverick Hunters who were going Maverick. No, it doesn't say explicitly that they were made fanatically loyal, but the high rate of Hunters going Maverick was the stated reason for their creation. I'll have to double check the manual when I get back to it, but that's what I remember of it.
 * Really? Let me know if you find it; if that's true then I might as well delete this one.
 * Found the manual, and it seems I misremembered it. The memo from Cain Labs in the manual states as Repliforce's directives:


 * I guess I interpreted that first one as them being made in response to Hunters going Maverick. The rest of the memo is an evaluation of how Repliforce was performing (not well; it calls them 'ineffective and potentially dangerous'), and further directives to find an alternative to Repliforce. In any case, your theory makes a ton of sense... which is probably why I'd assumed it was already canon.
 * Thanks for that. I'm rewriting my theory to make it more clear, anyway.

Reploids are not really robots
Reploids have DNA, can bleed, often are said to be hard or impossible to tell from humans in some games (particularly later post-X series; ZX Advent, for example, has a reploid and human main character who are more or less exactly the same). In adidtion, X himself is referred to as a Reploid even if he is the first. I speculate Reploids are grown in capsules with nanomachines, and the name Reploid refers to the fact they replicate living organisms, though most also have robotic parts or armor.
 * This is actually supported by some Mavericks; Toxic Seahorse turned himself into a form of goo to slip through a grate and then reformed, and Double transformed into his bigger self almost instantaneously. Could also explain how Axl can change forms too.
 * Indeed, Reploids and humans were at first only distinguished by very different outward appearances, the Reploids' superhuman traits and abilities, and the barrier between the two "species" that kept them separated in society at all times. However, Reploids are designed to look very human, and more importantly to think and feel like a human, not to mention the whole bleeding and DNA-having thing, so it's highly likely that regardless of the exact chemistry, Reploid bodies are every bit as complex as human bodies and use many identical systems. By ZX, it's explicitly stated that Reploids and humans are practically indistinguishable once the last major barriers are eliminated. This fits nicely with the way X's body, not just his mind, adapts to the things he encounters, much like an organic body.
 * Reploid is a portmanteu of replica android: they're replicas of X, who is technically the one true android (Zero may count, unless Wily went off in another direction). However, android just means 'humanlike,' roughly. Early Science Fiction often used the word android for what we would call clones, artificially produced humans, like the ones in Star Wars. 'Organic' basically just means molecules with carbon-oxygen bonds (well, for practical purposes) in chemistry. Organic molecules are very, very good at self-sustaining reactions at the molecular level, and nanites are supposed to be small, so taking advantage of those traits makes sense.
 * They could be like Cylons...

Repliforce was the reason humans started being so quick to label Reploids as Mavericks
When told to stand down, disarm, and come in for questioning, The Colonel, representing Repliforce, basically told X and Zero to piss off because of his and his troops' pride. Yeah, being forced to disarm is demeaning, especially if you're a bunch of Proud Warrior Race Guys, but they're an army. They're not supposed to tell their superiors to piss off. Maybe if he said X and Zero didn't have the authority to bring them in, if he said he's going to check with their superiors, something more reasonable than a robotic dick waggling (I'm assuming they refused to come in even after they told X and Zero to piss off, when the top brass told them to cut the crap and come in). Once it became clear Reploids would not do what they're told, even when they agreed to, humans became increasingly paranoid.
 * Forget not doing what they're told, and forget humans being paranoid. Repliforce was responsible for a lot of deaths and Sigma was involved. The question the world would have asked was, 'did reploids just help Sigma kill, destroy, etc.' willingly or was Repliforce really infected the whole time, the way it turned out the people in the initial rebellion were, and the virus was even better than they thought? Either way, Repliforce would have started a witch hunt and seriously hurt reploid morale as well as human.

The Repliforce refused to come in for questioning because General was covering his ass.
He ordered his troops not to come in for questioning (citing their unflinching pride as an excuse), because he didn't want to admit he was secretly meeting with a 15-foot tall shadowy figure that espoused violent revolution against humanity. The kind of thing a sensible officer would investigate or at the very least report to superiors. Granted, he didn't take up Sigma's offer, but he must have realized an investigation might have revealed these meetings and his lack of action, causing him to be court martialled. Because Repliforce's pride is so extensive, he couldn't face that indignity, especially in the face of his own troops, so he launched a military coup, causing numerous deaths and the destruction of his own army, just so his incompetence could be kept secret.
 * In fact, given his job description, and that what Sigma was suggesting was essentially high-treason, General might have been within legal right (even without knowing it was Sigma, wanted war-criminal) to have killed him on the spot.
 * Or, to go one step further, General knew that was Sigma and the entire thing was a plot to take Repliforce and defect. Flee the war against the mavericks, desert in the face of the enemy. Abandon the rest of the world to Mind Rape to save his own skin, and that of his men. If he laid the groundwork for that in Repliforce, it would explain Iris's last words.

Zero has multiple clones of himself.
It would sure explain a lot.

The Light Holograms are actually maintained by someone
I'm throwing out a personal idea that someone, likely of the Cossack dynasty, is secretly helping X, scattering his armors far and wide where X would appear and making new ones. However, they are guided by a sentient Light Hologram. They don't reveal themselves because there are a number of uncomfortable questions they don't want to answer, and they really don't want to turn themselves into targets for the Mavericks.
 * It could be Auto. Watch the Volt Catfish cutscene from the PSX version of X3 real closely.

Not only is Dr. Wily still around, the series will end with him winning.
Tatsunoko vs. Capcom revealed that he was around post X7, at least, since Axl was in the ending. Since X, Zero, and Axl don't know enough about him, they won't be alerted to his presence until it's too late. While Sigma dropped hints in X5 that let the viewers know who Wily was, the heroes are still clueless.

Wily is everywhere.
In X5, Sigma scattered the Virus all over earth. If, as Capcom said, Wily's consciousness is in the virus, that would mean he is everywhere.

Everything after X5 is a Lotus Eater Machine dream X is having...
...And in the inevitable X9, it will have 16-Bit graphics... But then it switches to 32-Bit in inopportune moments, and X is the only one that notices. The reason I say X is in a Lotus Eater Machine is that (while I haven't played the games...) there's a few contradictions or bad quality in X6 to X8, but why would these contradictions keep happening? And why did Zero come back to life? Simple, X refuses to believe his friend is gone, therefore he's trying to keep himself in a world where he feels like he's with his best friend, and Axl, he's never known him, he's just a spy thrown in the Lotus Eater Machine to make sure X doesn't catch on, and when it's revealed Axl is the final boss and you get to kill him in a One-Winged Angel, X will finally wake up, finally accepting that Zero, his long time friend, is no longer here...

Dr. Light knows Wily made Zero, but refuses to tell him.
I blame his pride. Zero seems to be a stronger combatant than X, but Light refuses to accept that Wily could one-up him and thus won't inform the robot of his creator.
 * I blame the fact that Zero's a hero, while Wily was a world-famous terrorist who built him solely to destroy. Not the sort of thing Zero would like to know about his creator. Also, Light dislikes fighting. He only built X with weapons in case there came a situation where he would need them.
 * There's also the fact that if Zero turned himself in, X no longer has help out there, and the Dr. Light AI's goal appears to be X's health and survival. He does seem to trust Zero, and even makes an armor to make him stronger, which doesn't exactly work with being jealous that Wily made a stronger robot. Generally, it's Wily that's jealous of Light, anyway, and constantly trying to one-up him.

Dr. Light's hologram is the first Cyber-elf.
Light figured out how to upload his consciousness to a computer, which allowed him to build the capsules for X. As of the end of X5, Light has upgraded himself to the point that he no longer needs capsules to manifest physically, and he later expanded on this technology to create the Cyber-elves to help fight the Mavericks.
 * However, this does raise the question of why Cyber-elves die when they use their powers when hologram!Light himself seems to be just fine appearing and giving you upgrades multiple times.
 * A property of the capsule, maybe? It would make sense that the Light-elf could be "recharged" while it lays dormant most of the time.
 * That works with X surviving as long as he can go back to his body and recharge in Zero. It's once it's destroyed that he starts dying as he uses up his energy.

X's father is actualy Kenny from South Park.
No matter what, in every game it is impossible not to die. Yes, you would have a fluke or two, but c'mon? On every level, there has to be a time where you encounter an event and then you die. To compare with Kenny, they both die easily when they encounter an enemy, a death hazard, or just come in countact with anything that's seemingly harmless. To include, they both RARELY remove their head gear. I think there should be a family reunion, or else Sigmas will summon out more mechanical walking birds to pick out X's pixelated eyes.

There is only one capsule.
I mean, really, what would make more sense? For there to be over 33-49 (calculated guesses for X-X5 and X-X8 for the number of capsules, respectively) capsules that just happen to be in areas that end up being outposts of the Mavericks (especially places built after Light could have placed the capsules); or for there to be but one capsule, that can find X (or Zero in X5) and give him what he needs as he needs it, and then move on (ever notice how the capsule disappears after you use it)? One capsule would also render hologram!Light's sapience feasible, and also explain how the later armors can keep on par with and even supersede recent robotics. (There is a good bit of dormant time as a capsule, after all.) (Except for those two arm ones in X4; they are probably different though, as they stick around.)

== There were initially only maybe four or five capsules. However, they replicate themselves through nanomachines. Furthermore, the Light Holograms themselves are the ones who create new armour upgrades. ==

I think this makes the most amount of sense. The capsules themselves can't be all that complicated to make, considering how many there are. Dr. Light probably created a mechanism that allowed his capsules to constantly replicate and spread throughout the world. The armors are all probably created in a similar fashion. If the Dr. Light Holograms truly are sentient, they could theoretically create new armours for X as time goes on. This would make sense, since if X truly has unlimited potential, he should reach a point where new armour upgrades are unnecessary. Since the Light Holograms constantly create new weapons and armour depending on the time and advancements in technology, it would mean that X would always have the latest and best arsenal at his command. This is further backed up by how the Dr. Light Hologram was able to create an upgrade for Zero. The capsules are all probably connected to X in some way. When X was sent out on an infiltration mission in Command Mission, the capsules created an armour that would be best suited for sneaking missions, and reformatted X on their own.

Light's Hologram was built into X the whole time; the capsules are just maintenance terminals that any reploid can use.
X5's ending seems to indicate that Light doesn't need a capsule to appear. Going with some of the above WMG's, X has the ability to create entirely new weapons rather than simply copying them like the original Mega Man. Perhaps Light's hologram is a representation of that ability, passively gathering small pieces of tech data and occasionally assembling it into an upgrade that X can use, usually (but not always) by hijacking and overclocking a nearby capsule to provide the upgrade.

As for why Zero can also see him from X4 onwards, maybe the Light program copied itself over to Zero after spending so much time with X, like a benevolent version of the Maverick virus. It couldn't create upgrades for Zero until it could study his hardware from the inside out; hence the lack of upgrades for him up until X5.
 * Or alternatively, Dr. Light uploaded his brain into Cyberspace, but being the scientific genius that he is, was able to access some sort of "back door" in both X and Zero's programming, thus allowing him to keep an eye on them if needed.
 * Actually, though, if you know what a "Zero Space" or "Area Zero" is, how Light can come out of his capsule can be explained—because of the merger of the Cyberspace and the real world, Light's hologram appears in the same way that Phantom appears in the Cyberspace in Zero 3, and he can freely move around this time.

Copy Zero's (i.e. the hero in MMZ) "buster" is Axl's gun
As there's no MMZ WMG page, here it is. Axl will go nuts due to Lumine's parting gift, and X and Zero will put him down. Then, Zero will get sealed, and his "original" body will be appropriated by Weil to make Omega. When Copy Zero is built to host Zero's programming, he doesn't have an arm cannon, so they give him Axl's old gun to go with his beam saber.
 * Doubtful. Zero picked up a nearby fallen Resistance Fighter's gun. His Buster is just an ordinary Buster Gun that's been modified to use the Z-Saber as a power source.
 * So if Zero picked the gun off a dead resistance member, what exactly is Omega using then? Really I think the gun is his actual Z-Buster but under the different art direction for the sake of looking cool. Axl's guns look more like modified Kimber pistols than MMZ's seemingly futuristic sub-machine gun design.

Taking the above theory one step further: Copy Zero's body was originally Axl's.
For whatever reason, Lumine and Omega awaken at around the same time, and X will have to face both of them alone. After defeating Lumine, Axl will take back his body long enough to tell X to wipe his memory clean and use his body to save Zero. Through some tweaking, Axl's body takes on a form that seems to be a cross between him and the original Zero (red-on-black instead of red-on-white).
 * Zero would have to undergo a fairly radical transformation to purge itself of the virus. Then there's the whole thing about about compatibility issues. It might take a body like Axl's to be able to first copy Zero's well enough for the transplant, and then change itself over time.

The X series is an alternate future for the classic series.
There's a radical change in tone between the classic and X series. The classic series is bubbly and happy while the X series has people dying left and right. Dr. Wily is significantly more malevolent as far as the X series is concerned compared to his portrayal in the classic series. The X series is basically a "bad future", an alternate timeline that branches off from the classic series. Furthermore, the Zero series is also an alternate future, allowing the X series to continue on and on like the franchise zombie that it is while the Zero series branches off somewhere along the line.
 * Or maybe things just got Darker and Edgier when Dr. Light, known as a champion for ethical treatment and use of robotics, died.

The entire X and Z series take place in X's head while in his "30+ years" of stasis.
Dr. Light programmed a series of recurring challenges based on his own experience with Dr. Wily—that, or the simulation was only supposed to run once, but X wasn't satisfied with how the first game ended, so each sequel was an attempt at a Fix Fic that went horribly wrong for whatever reason. Eventually he goes insane from the effort and (still in the simulation, mind you) decides that Humans Are the Real Monsters... except he can't bring himself to go through with it and has "Zero" take up the reins in his place.

The entire Mega Man series takes place in X's head while in his "30+ years" of stasis
When Dr Light created X, he decided that X needed to be ready for every scenario. Each game represents a different lesson for X, so he can awake as a matured individual.
 * The Mega Man series is an idealised version of what actually happened, to form a basic sense of morality. In reality, Dr .Wily was either far worse, or rather tragic.
 * The X series is a Darker and Edgier edition, that has become more developed to identity moral ambiguity. It also serves as a prediction for what will happen when he awakes. The virus is X's attempt to rationalize why someone would turn bad, while the New Generation Reploids and the Mavericks in Maverick Hunter X show that he's recognizing moral ambiguity.
 * The Zero series enforces the closest system to Real Life morality. It also introduces how evil someone can get. This is what Dr. Weil is there for: he's basically the absolute worst representation of the human species. Copy X is basically warning X not to go too far.
 * The ZX series reconciles things.
 * The Legends Series is the theoretical doomsday event.

The X series calendar is hexatridecimal (Base 36)
When it reads that X was constructed by Light in the year "20XX", it doesn't mean "some unknown year in the 21st century." It means, literally, 20XX: the year 94533 on the Gregorian calendar. 200X, the year Protoman was created, would be the Gregorian year 93345..."a mere" 1,188 Gregorian years before. By this distant day, humans live as long as, if not longer than, Biblical characters such as the Antediluvian peoples, ~1,000. The reason humanity is not ridiculously far out into the galaxy or beyond is because of 1) the rise and fall of civilizations occuring at a rate just as often as previous human history, 2) there being no such thing as Star Trek/Star Wars "warp" or "hyperspace" travel, of at least the kind that wouldn't crush biological matter into tiny particles; i.e., think Orson Scott Card's Ender's Game, and 3) outer space is mind-shatteringly gigantic.

Actually, to tell the truth, there is no evidence whatsoever to prove that the events in question do not take place on a planet called Earth, but completely different in all but name from our own. In fact, if the story given by The Protomen were to be taken at face value and then further elaborated on, "Reploids" might very well have been the term the planet's inhabitants used for their version of the Cylons, and the whole planet is in fact the nuclear wasteland Thirteenth Colony that was encountered by the Caprican/Cylon refugee ships as they searched for a new home, a hundred thousand years before the present day... which of course reminds one once again of numbers such as 93345, and 94533. Who's to say that the recurring cycle isn't a lot older than the Capricans (nevermind Terrans) thought it was?

Zero never came back to life after X5.
This one's related to one of the above WMGs, but without the Lotus Eater Machine. Instead, X fulfills both his and Zero's role, imagining Zero doing the things he believes he isn't strong enough to do himself. Consider that when Zero "comes back", he supposedly has a new saber of his own, and a completely different fighting style. This doesn't make sense, unless it's really X all along, using a saber fighting style of his own. This also explains why all of the plot threads related to Zero's past suddenly drop off for the rest of the X series.

It's also possible, that Zero's essence literally exists within X via the Saber. Note that in Zero, Zero's memories only start to come back when Cyber-X returns the saber to him. Obviously, the all-important control chip, or at least a back-up unit, is housed within the Saber.

Now, the only question remaining is how Zero's copy body is made. Simple: At some point between X8 and The Elf Wars, X realizes that he and Zero "have been the same person" all along, either by the inconsistencies becoming too numerous to ignore, or by accepting the truth that he is a hero in his own right, and that he must stop relying on Zero if his own strength is to flourish.

And then Weil digs up Zero's body and turns him into Omega.

X realizes that he and Axl alone aren't enough to combat this threat (especially if Axl has fallen in battle by this point), so he has Alia, a known expert reploid designer, apply all of her skills towards building a new body for Zero, utilizing whatever new technologies have been developed since X5 to make "Copy Zero" a match for Omega in combat, with the added bonus of being completely virus-free. He then returns the Z-Saber to Copy Zero, essentially restoring Zero to life. They fight the Elf War, and at the end, defeat and seal up Omega. Weil is tried and exiled into space, along with the dormant Omega.

Zero decides he should be sealed back up, not because of spreading the virus, but because his mere living seems to bring conflict. Giving the saber to X once again, Copy Zero is sealed in the underground lab, leaving the world in X's hands... until X is forced to sacrifice his body to seal the Dark Elf.


 * Well, that's crazy. But one thing to note here is that the one who made Zero's copy body is Ciel's ancestor. Who exactly the ancestor is is never touched upon, but it's definitely not Alia (Alia is a Reploid and Ciel is a human, you know.) As in how Zero's memories seem to "come back" when he retrieved the saber, it might be just a coincidence.

The Mother Elf was designed to end the Maverick Wars, not by killing Sigma, but by erasing his DNA from the copy chips of all the New-Generation reploids.
Word of God has confirmed that X8 is canon, which creates a massive plot hole with The Mother Elf's role in ending the Maverick War. Unless, of course, one remembers that Sigma's DNA is in every single Copy-Reploid, and even if they discontinue manufacturing them, there were enough of these reploids to build an elevator into space. And many may not be inherently evil, and given the Repliforce debacle, justifying the destruction of all these reploids is impossible. However, the fact remains that any of them could conceivably become Sigma at any time, so a way needs to be found to remove the DNA from their copy chips.
 * Well, she'd have needed to erase the virus from everyone anyway in order to permanently destroy Sigma/the Sigma Virus. So what real difference do the New-Gens make?
 * @ the theory itself: This is confirmed in the Mega Man Zero Official Complete Works. Indeed, the Mother Elf works by deleting the Sigma Virus.

Lifesaver was killed by Zero in X5.
He's completely absent from X6, and the last time he's seen in X5 is when he's with X at the Zero vs. X fight. Either he was killed by Zero in a maverick-induced rage, or indirectly killed as collateral damage when fighting X. It continues the cycle of Zero attacking and killing his teammates.
 * I'd say that Lifesavor got court-martialed and fired from the Maverick Hunters. He was explicitly told by his superior to keep something a secret, deliberately disobeyed orders and snitched to X anyway, resulting in a situation of distrust that nearly got two high-ranking Hunters killed. I'd be amazed if he wasn't sent to jail or declared Maverick for that.

The Zero Nightmare is the fake Zero built by the X-Hunters in X2.
Although it was destroyed, Gate rebuilt and used parts of Zero's DNA to make it more life-like and effective. However, the Zero Nightmare is weak to the Z-saber, just like how the fake Zero in X2 was instantly killed by Zero.

The entire Repliforce in X4 were Mavericks.
After the Sky Lagoon falls, Colonel refuses to disarm because they were actually responsible, NOT because of fanatical loyalty. The loyalty part was just a cover. All the events of the game done by Sigma/Sigma's mavericks were actually planned. That suggests that Magma Dragoon, Cyber Peacock, and Split Mushroom were not any "more" maverick than the rest of Repliforce.

After Iris's defeat, she claims she wants a world for reploids. So does Sigma. In the Memorial Hall mid-stage, Colonel actively tries to kill X, unprovoked. Typical maverick behavior, but importantly, Repliforce really has no justification for having a satelite weapon besides that they're terrorists.
 * Except that Iris wants a separate world for reploids, while Sigma wants to Kill All Humans first (he claims that humans are limiting Reploids' evolution). As for Repliforce's behavior, they're not Mavericks (as in, reploids who's infected by The Virus), but they act like one, because of their severe Honor Before Reason.
 * Not just that, Colonel is seen to be the most unsympathetic of the Repliforce. Even General pulls out a Redemption Equals Death to stop Final Weapon.
 * Additionally, I don't think Final Weapon belonged to Repliforce initially. They took it over during the game.
 * OBJECTION—in one cutscene, General DID meet Sigma. However, Sigma never revealed his identity to General when they met.

The many definitions of a Maverick
Trying to sum it all up:
 * 1) The old definition of "maverick": Reploids whose minds defect because of some malfunction in their circuit. (You know, being cheap replicas of X, this tends to happen to most early Reploids. Also Vile, though he later arguably became type 3.)
 * 2) Viral Maverick: Reploids whose minds defect because of viral infection. (most animaloid Reploids, Sigma, Gate (by Zero's DNA))
 * 3) Free-Will Maverick (or just "having evil intentions"): Just genuinely evil, like real life criminals. (Dynamo, Double, arguably Red and Doppler, High Max, The Nightmare Police (X3), Serges, Violen, and Agile (X2), and arguably animal Reploids in X1, X2, and X7)
 * 4) Misblamed/Political Maverick: Reploids who don't qualify as any of the above, but get accused as one. (Repliforce, for example, and animaloids in X6, though (possibly) later they're also infected.)
 * 5) New-Gen Maverick: Having Sigma's DNA, New-Gen Reploids can "wreck their own mind by themselves". (animaloids in X8, Lumine, Colonel Redips)
 * Repliforce, if not Mavericks, then they were still bloody stupid and largely responsible through their own actions for much of the destruction that followed.
 * I think that some of the animal reploids there is some varying degree of maverickness between viral Mavericks, free-willed Mavericks, and deep-cover operatives.

Had the Maverick Hunter X series continued...
Zero wouldn't have been the last creation of Dr. Wily. Instead, he would've been a normal reploid, discovered by the X-Hunters to be just clinging to life, and overhauled by Serges after the X-Hunters found some leftover tech of Wily's. Zero's nightmares would be revealed to be incomplete false memories to brainwash Zero, with various references to Wily being attempts by Sigma to manipulate X and Zero into fighting each other to see who was the best. After fighting off the anti-virus from X3, Sigma would've been so damaged that even he believed the fake story. Even after X6 and Inafune was involved again, he didn't really try to bring Wily up again, not even in the Zero series.

X is still a B-Class hunter by choice.
This is the guy who iced Sigma more than once, something even Zero wasn't able to do until at least X4. You'd think he'd deserve at least an A rank by now. The reason he doesn't want anything more than a B rank is that he doesn't want the other hunters to feel like they have to compete with him, or he doesn't think he should be rewarded for causing all the kinds of violence that he was created to stop.
 * (applause)
 * Wow, that makes a damn lot of sense. I can see X constantly refusing promotions/medals/perks usually given to other Hunters on ethical grounds.
 * By X8, though, he and Zero are both finally promoted to S-Class. This isn't going against this theory, though, because remember, he dropped out of battle before X7 only to come back in during the Red Alert conflict, having accepted the necessity of taking care of business again.

Animal Reploids are on an even lower social class than humanoid Reploids
We know there are humanoid Reploids with immense power, so why bother building something as impractical as a ten foot mammoth or a dragonfly one when you make a normal-sized human one with the appropriate equipment? The answer is to make a subordinate class of Reploids, reflecting the relationship between humans and animals. That's why the first bosses are always animal types; they know they're on the low end of the totem pole and believe that if they defeat the heroes, they'll move into a higher station. And given the villains' collective "evolution" mindset, it's also why they throw them at the heroes first: they're weeding out those they think are too weak for their new world.
 * Alternatively, Sigma provides them escape from the Fantastic Racism. He basically says to them "You can continue your lives as low-level Reploids, or you can join me and make a better world for yourselves.

Reploids face their own interspecies discrimination
(Inspired by above) Considering what we've seen in the series so far, reploids are capable of being smug assholes as much as anyone else, and there seems to be a running theme of 'evolving' or being a superior reploid. It therefore seems likely that there is tension between class distinctions of reploids. For example, powerful elite reploids made in special labs probably think themselves better than mass-produced reploids, who in turn think the elites are Mavericks waiting to happen. Scientist reploids who make other reploids tend to treat their creations like tools and monuments to their genius, rather than people. Humanoid reploids think that all animaloid reploids are just Maverick time-bombs while animaloids think human-like reploids are 'suck-ups' to the humans. X's dream of creating a world where humans and reploids co-exist isn't just about repairing relations between species, but stopping discrimination among reploids themselves.

Sigma is John McCain in disguise.
That, or McCain cyborgized himself and used the codename "Sigma". Well, he's "the Original Maverick", you know.

How Sigma can possibly come back.
Since he's
 * This explains why no-one has tried to colonize other worlds, even by the time of VideoGame/MegaManZX.

Axl really did die in X8.
Lumine did a final attack on Axl that knocked him out - really, Axl was killed by Lumine, which explains his absence in Zero. The Axl in Command Mission is either a clone, or the game was set before X8.
 * The latter is correct.

Lumine wasn't the Man Behind the Man.
It was Sigma. After countless Death Is Cheap moments, Sigma began to realise that he would soon be Deader Than Dead. Not wanting to simply die, Sigma manipulated the Copy Chips. This way, the New Generation Reploids would at least contain his soul and ambitions-not even total death would stop his goals. Lumine was designed as a sucsessor, someone to order his legacy. Lumine was but an Unwitting Pawn, blissfully unaware that his ideals were Sigma's.
 * This can actually be right...

Alternatively, Lumine really was the Man Behind the Man.
No where is it even so much as hinted at that Sigma manipulated the Copy Chips. Besides, if Sigma used Lumine, then how did the latter have full awareness of almost everything that was happening? Especially when you take into consideration how Lumine used X and the gang to do most of his dirty work for him, it's painfully obvious that Lumine really is the evil genius that he's built up to be.

The countless battles are why X was planned to be the main villain in Zero.
Infuane did mention he planned for X to have a Face Heel Turn instead of an Evil Knockoff. In this original timeline, X went mad from having to retire hundreds of Mavericks, and countless humans dying. Over time,he went mad, and abandoned the belief that peace could exist between the two. Despite this,he organised a copy,designed to be a more heroic and idealized version of him. The true X now believes that humans will only be protected if Reploids are crushed out of the equation.
 * Then why did he make a copy in the first place? In original Inafune's story, there's no copy.
 * Oh right. But that doesn't explain what or who imprisoned the Dark Elf.
 * Was the Dark Elf even part of Inafune's original plan? Remember, this series was hit pretty hard from the Executive Meddling that brought Zero and Sigma back for X6.

Dr Wily Came Back Wrong.
From what is implied, it seems Wily has changed a lot from when we last saw him. A Mad Scientist with the standard world domination plan, becoming an Omnicidal Maniac bent on razing the world with Zero. This is because the process of becoming part of the virus has screwed around with his mind. Similar to how Sigma became more and more obsessed with killing his enemies, not to mention the Motive Decay, so did Wily turn into a warped version of himself. All that's left of his personality is a revenge-filled maniac, who wants the world to burn because he lost. This is why Omega is so Ax Crazy.
 * It seems like you're confusing Dr. Wily with Dr. Weil. Weil was the one who turned original!Zero into Omega, not Wily.

Vile is a rebuilt Bass, after the raid of Wily's lab.
Vile's habit of property damage and torture may stem from the fact that his suffering circuit was attached to something that was simultaneously outdated and made for war, he could have trouble trying to understand the signals, or actually remove them. We can't see his face, so they could have repaired his body armor by using a spare Sniper Joe. Not to mention he has a a thing for X, which means he needed an expanded backstory for X besides blind Ax Crazy tendencies to "always" hate him. Wrap it up with his Ride Armor to get his Combining Mecha fix as his replacement for Treble, and there you go.

Ciel is Zero's version of Roll Classic.
Note the golden hair, blue eyes, and pink outfitting. They both serve as the important female characters of their respective series. Also, as in [[Mega Man Legends Legends}}'s Roll Caskett, Ciel is a talented mechanic, having built Copy X at a young age.

Similarly, Zero is X's version of Proto Man.
They both have red in their armor. Also, like Proto Man, Zero is disobedient and independent. After first awakening from the capsule Wily seals him in, Zero acts like a Maverick, killing those who enter Wily's lair. Proto Man began as an antagonist (albeit inadvertently), serving under Wily as Break Man. Eventually, like Zero, he joined the good guys.

Zero is a Manchurian Agent.
It seems odd that, after Sigma beats him, Zero has a Heel Face Turn. The truth is...he didn't. Dr Wily had the raw power of Omega, but he didn't have the skills or intelligence. This is why Zero exists: to gain all the intelligence and pragmatism needed to destroy all enemies from within. After all, what's more dangerous than the Axe Crazy Omega? An Axe Crazy Omega who's scheming, intelligent, and Dangerously Genre Savvy. The Maverick Zero you see in the bad ending is this. The reason why Omega remains a puppet of Dr. Weil is because the Zero personality is gone.

Alternately, Zero "turned good" because his programming, like his body, is based on X's.
Wily started with a stolen copy of X's source code and made his own adjustments, thinking that it would be ideal for a new robot master since X wasn't hard-coded with the Three Laws. And it worked; without the morality training that X received, Zero became the ultimate war machine. However, after a while, the latent parts of X's programming (namely those annoying "free will" and "empathy" routines) started rebelling against Wily's modifications, culminating with the aftermath of the Sigma fight, where Zero's X-based programming took over, creating Zero's heroic persona.
 * Alternatively, Wily ended up adding free will anyway, since it would make Zero more efficent. However it also meant Zero could choose to be good...
 * That's a great theory and all, but the X-based programming ain't gonna turn itself on whenever it wants. Also at that point Zero seemed to be enjoying his killing spree and never seem conflicted about it. It seems illogical to suddenly decide to be good after getting what looks to be like a major headache. This troper believes that it had to be triggered some way, via the battle with Sigma. It could be that Dr. Light suspected through all those years of living that Wily will never stop his ambition of world domination (even after he's dead) and will create a robot to fulfill that dream. Upon making X, Dr. Light installed a program designed to specifically effect Dr. Wily's robot (Dr. Light and Wily have worked together in the past so it's probably not too hard for Light to figure out how to create a program to counter Wily's programming) (Note: I typed 'specifically' because it ONLY effects Zero. This would make sense on the basis that all the reploid copies made by Dr. Cain are not effected by this programming because they are not perfectly modeled after X therefore not fully compatible with the program, but still able to carry it besides if everyone was compatible then we'd have no bad guy). This program was passed on from X to Sigma and infected Zero during their battle. It is possibly around the time where Zero severed Sigma's arm where the program could have transferred.Their battle can be seen here. Upon activation the program started fighting off Wily's programming and Sigma took the opportunity to smash the area on his head where the W appeared (probably where main programming lies) thus the X-based programming gain control of Zero however because Sigma smashed the area containing Wily's programing Sigma got infected with the virus.
 * Also adding more to the above, it could be that Dr. Light knew that there was a chance that Wily will create a robot far stronger than X since Wily designs his robots to be weapons of mass destruction while Light tends to create robots of convenience. Light thought that if it Zero ever managed to destroy X then X will infect Zero with the X-based programming. It's a great back-up plan and it seems plausible since in all the battles where X fought Maverick Zero, Zero ALWAYS reverts back after the battle. Though that's just 2 battles, one in MMX 2 (where you fail to collect all of Zero's parts) and one in MMX 5 (where you fail to destroy the space colony.)
 * Even if his design was unique, he would've turned good anyway. Without any memories of his true identity or under Wily's control, he could be free to choose his own personality. Dr Cain and X were smart enough to be nice to him, so he didn't go evil again.

Zero DID really die in X5.
Here's what really happened at the beginning of X6: Gate finds Zero's DNA and shares discovery with Isoc. After creating High Max and the Nightmare, Gate is satisfied - Isoc is not. Isoc returns to the crash site and finds Zero's body, or the largest remaining amount of it. He reconstructs any missing parts and infuses Zero with Nightmare Souls, attempting to have Zero at his command. And it succeeds - at first. There's still too much Maverick Virus lingering around from the Eurasia crash, which triggers Zero's maverick virus symptoms, and the Maverick virus battles the Nightmare Virus for control of Zero. This explains why his pre-battle dialogue is so bipolar - when he speaks normally, the Nightmare Virus is in control (when he tries to join or trick X). When he speaks in all caps ("BLUE LIGHT KILL KILL") the Maverick Virus is in control.

Realizing his puppet has run amok, Isoc gives the speech about "Zero's Ghost" as a cover-up. Isoc DOES tell Gate he's seen Zero in private, before Zero's "return". Isoc knows "everything about Zero" - if he's the one who zombified him, him paralyzing Zero after Zero defeats High Max (with purple energy) can be seen as Isoc using the Nightmare virus in Zero's system to hold him in place.

X only finds Zero in X6 after defeating the Zero Nightmare, or at the end of the game after defeating Sigma (and at this point, it can be assumed that the Nightmare system has been destroyed). When X attacks the Zero Nightmare with Zero's Z-Saber, the Saber's impact causes Zero to remember more of his non-virus memories - causing him pain, as now three personalities are clashing. When the Zero Nightmare is defeated, THEN Zero goes and hides while he repairs himself! Possibly survival instinct (run and hide), or being wary - if X knew that Zero Nightmare was in fact Zero, he might have regret attacking him, or paranoia that Zero is now a Nightmare Virus carrier, and would require all sorts of scans - see X's approach in X5 - both responses Zero doesn't want to cause. After this brief repair period, both virus personalities have been subdued enough that the main Zero is in control. Zero is partly amnesiac, due to the Nightmare system corrupting most of his memories. He doesn't remember any part of being the Zero Nightmare, as he doesn't remember being revived by Isoc. He doesn't remember any of the events before X5 - which is why Wily, Iris, and other plot points are never brought up again, and also forgot most of his fighting style (resulting in the change in ex skills). Being partly amnesiac takes some of the edge off his hot-headed personality (he speaks with a great deal of ellipses), although he starts to get over his missing memories in the later games.

In X6, Isoc attempted to enter Sigma's body.
Given that he's not shown to have any fighting abilities, once X/Zero defeats Gate he realizes he's trapped. When Sigma first appears, he speaks normally and acts in-character. After he kills Gate, Isoc ejects his consciousness/program/etc. into Sigma and attempts to control him with the Nightmare Virus. He's unsuccessful, and the Sigma Virus then proceeds to Mind Rape both personalities, causing Sigma's insanity to develop during the time before the final boss. Suggested by Isoc's original body having "no response" and similar to the erasure incident.

Douglas and Lifesaver's disappearance from future games is because...
They're either gone Maverick or were Killed Off for Real. One does not expect a war where The Virus is rampant and not experience a few casualties, you know. Consider this, as well....Lifesaver was a normally obedient Reploid, only to blatantly go against orders from Signas and instigate a fight between X and Zero, and even following X to an incredibly virus-infected arena to confront Zero! As for Douglas, I'd assume that he was a casualty from getting into contact with an infected Reploid (as he was the mechanic of the group.)
 * Or, alternatively, Lifesaver was fired for his actions.

Zero houses the consciousness of the Evil Robot from Mega Man 8.
Zero's malevolent super form and original berserker attitude are influenced by the Evil Robot, and every single act of hatred and destruction on the planet Earth since his crash-landing has been precipitated indirectly by him so that it could breed Evil Energy and restore him to life. It's possible when Wily made Zero, the Evil Robot used him as a replacement body, but was never strong enough to fully take over, putting Zero in a deranged state of bloody incoherent madness. Wily put the restrain program on him not just as a means of keeping him from betraying him, but because he knew from analysis and use of the Evil Energy that the Evil Robot was a million times more deadly than any of his other creations combined, even Bass, and if it gained control of Zero, it would be anarchy. Wily somehow tried to "shelve" the Evil Robot's personality but failed, and put a fail-safe mechanism on Zero's capsule so that in case he died, Zero would continue his mission of revenge in his stead. However, Zero grew so bellicose that he would attack everything and everyone- all because the Evil Robot needing him to stir up carnage to rejuvenate his remains. Sigma punched a protective cover on Zero's helmet, which caused his fist to make raw contact with the Evil Robot and either transfer to him like a parasite and erode his mind, or steal his power while the robot went all but dormant in Zero. However, in X5, contact with the Maverick Virus gave the Evil Robot new life until Zero was defeated. He could've been implanted in Omega from there, or Lumine, Weil, any number of villains, really. In the end, the Evil Robot will somehow procure a new body and attempt to exterminate all of planet Earth, forcing the current Mega Man to do battle with a nigh-unstoppable evil force. Finally, the Evil Robot could've been a scientist or machine created by some unknown force for evil and rebelled, a robot that experimented/was infused with Evil Energy and became power-mad, suffered exposure to it, or is out to kill everything out of fear of a universe-ending crisis a la Spiral Nemesis-style. Okay, mind: shut off now. This is getting crazier by the second!

In Maverick Hunter X, Sigma was not infected by the Maverick Virus.
He didn't seem to show any irrational signs, and is more of a Visionary Villain. Not to mention that the Mavericks that appear have genuine reason beyond "lol crazy with the virus". It would fit. As for why he survives in the credits, Sigma is probably smart enough to implant the ability to Body Surf via wireless transmitter and back-up bodies.

Any Viral Maverick can come back to the dead, not just Sigma.
All they need to do is replicate themselves during death, and transfer to another body. The reason why Sigma is the only one to do it on a regular basis is because of the emotional trauma of death. They return only due to loyalty to Sigma, and that can only last one death. The pain of getting killed, even if they explode afterwards(which is probably to make it hurt less), plus the seperation from their body makes them want to retreat into cyberspace. Sigma is able to come back due to his sheer fortitude and being a virus, while Vile is so Axe Crazy he doesn't notice the pain/is a Combat Sadomasochist. With Sigma, he probably

"Zero is Wily's creation" is just Sigma's ploy.
The flashback scene was merely Zero's Fake Memories implanted in X2, where Serges tampered with his schematics (where else did Zero get his Z-Saber?) The real story may be that Zero was a reploid just like Vile, with only a small defect to make him berserk. The real story on how Sigma discovered Wily's presence was that the warehouse merely set the stage, and after defeating Zero and noticing his surroundings, just wanted to discover who this "X" guy really is. He reads up upon Wily's profile and life before Reploid creation, and goes out on a slight. Come X2, he was rebuilt by the X-Hunters, who were really lead by Serges. Considering "Wily is Serges" above is true, he informs Sigma about his own plan, and reveals his plan to make Zero a Manchurian Agent. They set up the events of X2, and give Zero the perception that he remembers X and Cain. Come X5, where fake Zero dies off, original Zero and his Double Agent self "split" into the Zero Nightmare and Omega. So, come slightly before the Elf Wars, Zero seals himself off, not knowing that Omega, Serges' work, is biding his time, sleeping as a Cyber-Elf.

Vile/VAVA is not a Reploid, but a cleverly disguised Human+ test subject.
We have never seen his face, has humanlike proportions, a mecha in X1 and X3 is included in a Cargo Ship, and most of his weapons on the exterior. Perhaps Reploids aren't that mechanical after all.