Mega Man Zero/WMG

"You know, X has many Ho Yay moment with Zero in X series. And then the Four Guardians are created, using X's DNA as a base. As a result, three of them loves fighting Zero. Leviathan got the dominant homogeneous alelle, since her expression towards Zero is the most prominent among her siblings, and not to mention her being blue, like her "father". Fefnir and Harpuia got the heterogeneous alelle, and Phantom got the recessive homogeneous one, since he isn't too interested in fighting Zero."
 * Could Elpizo be the last host of Sigma's personality? My proof: "I did it! I did it at last! I destroyed X at last!" How could it be an "at last" if he had only known X was the seal for a few hours? Considering that he's compared to Sigma in-game as well... could it be possible?
 * "At last" more probably refers to his goal: Acquiring the Dark Elf. He know that if he want to do that, he has to destroy X.
 * "Few hours"? You seriously don't think the amount of time that passes in real life is the same as time that passes in the story, do you? But yeah, what the above poster said. Dude went through a lot of crap to release the Dark Elf.
 * I don't think that he's a host(remember, the Sigma Virus had been purged thanks to the Mother Elf), but I would say he's at least sympathetic to Sigma.
 * I just want to say two things before I start this. First, I hate slash pairings. Second, I'm not a yaoi fan AT ALL. Now that that's out of the way... Could it be that the Four Guardians' attitudes towards Zero, which range from Blood Knight, In Love With Your Carnage, Worthy Opponent, and Yandere, imply that X had feelings for Zero? They are all based on him after all... Seriously, just think about it. And remember those two things I said at the beginning.
 * I could agree with you. Heck, this troper even made a WMG about it:


 * Just to add more fuel to this, if the Mega Man Network Wiki is to be believed, the MMZ Collection site reveals that the Four Guardians aren't just based on X's DNA, they're based on part of his soul.
 * The same thing occurred to me, but I prefer not to think about it for the same reasons as the original troper. If we want to go that route though, X's moments with Zero were never that... violent. And Leviathan is female. What part of X's soul did she get?
 * This different troper tries to explain it: Leviathan's "soul" is probably also male, but then she ended up in a female body. (Can qualify for The Mind Is a Plaything of The Body, but there's no clear evidence for that.) Nobody knows why they use a female body, though. The violence is because she (and her fellow Guardians) only knows Zero as their enemy at first. Alternatively, X's pacifism holds out those violent "passions"; since he was split into 5, the emotions are separated. His original gentle and pacifist self (as well as his own memories) becomes the Elf X, while his "hidden selves" become the Guardians.
 * Or X didn't want to seem gay, and thus Leviathan was made female. Or for a reason that made Sigmund Freud spin in his grave.
 * Leviathan inherited X's childish aspects. Accordingg the the MMZ wikia, Leviathan doesn't particullary enjoy violence that much, but shes thourougly enjoys fighting Zero, being very playful about it as if their battle is a game. Word of God states that one of the biggest regrets of the development team was that they didn't adequetly flesh out Leviathan's (and to a lesser extent Fefnir's) personalities.
 * There's a pretty easy explanation for that - they are reploids, robots without programmed gender, and thus whether they are "male" or "female" depends on their bodies (since others would expect those in male bodies to be men and those in female ones to be women). So it is a case of The Mind Is a Plaything of The Body, but a justified one, and to be honest, there are many humans who behave the way they do purely because others expect them to, so it's not like it was pulled out of the ass. And besides, it's not like their love has to be romantic. Good friends "love" each other too, though they won't admit it loud.
 * X and Zero already behaved like a gay couple in the X series, so there's no big change...

Zero isn't the original Zero, in body or mind.
This is why Zero no longer inhabits his original body. For whatever reason, the original Zero was killed. They were incapable of bringing back the original mind, so they instead opted to make a perfect replica of Zero's personality. It sucseeded. They also

Weil wasn't allways evil.
Sure, the game established him well as a Complete Monster, and many fans agree with that so much that it's arguably not even subjective. But let's check the manual: The humans feared that the Maverick Wars would happen, so he created the Project Elpizo, a project to create a Reploid to be a perfect ruler (the function of Omega) by using the Mother Elf's program rewriting ability to control all Reploids in the world, avoiding them from becoming Mavericks. Sounds like a good idea, right? But as he said himself in the game, "The joy of ruling all that you see... Only a human could possibly understand!" And, considering of the nature of the project (Brainwashing for The Greater Good), put the two together and... With Great Power Comes Great Insanity - he then Jumped Off the Slippery Slope and instigated the Elf Wars. And as he pointed out (and as the Caravan shows us), the most other humans are actually Not So Different from him - they all want to end all the Maverick problems, and they think that Reploids are Just Machines and must subdue to the humans' will. To sum it up, he was a Well-Intentioned Extremist (heck, his methods wasn't so much extreme), but then he crossed the Moral Event Horizon by creating the war in the first place.
 * Or he crossed the Moral Event Horizon after the war. Most of the war's casualities are hinted to be because of the Dark Elf and Omega(who are pretty Ax Crazy to begin with). Plus, given the outcome, it would be expected to exaggerate his actions. Not to mention the kind of punishment Weil got would drive anyone to losing all sense of humanity. This makes Weil somewhat of an even more chilling villain: someone who is utterly depraved, yet his backstory and original methods make him relatable. And thus, more disturbing.

Wily has long since given up trying to make Zero have a Heel Face Turn.
Think about it: Zero is the beloved hero of the planet, and the legendary Reploid. He ends up saving the planet from a Complete Monster. At this point, he's eclipsed Mega Man X. Much of what motivates Wily's actions is trying to one-up Dr Light, which he's sucsessfully managed. At this point, Wily is probably quite proud at what Zero has done. Given the "Wily and Master Albert are the same person" theory, he doesn't even need Zero to conquer the world.

Omega is not an original consciousness created by Weil but rather the personification of the Zero Virus. So technically he is Zero, in a sense.
When Zero's consciousness was removed from his body for the purpose of studying the virus in his body before the Elf Wars the Zero Virus took over and decided to follow Wily's original programming and as a result went on a rampage. Weil in the illusion of peace created an armor that would suppress Zero's original body and all of its horrible powers and was granted the right to continue the virus research. When the time arrived Weil released the Zero Virus, now named Omega, which corrupted the Mother Elf into the Dark Elf and started the Elf Wars. The possibility that Omega is the Zero Virus is supported by the fact that his presence warps reality and merges the real world with Cyber Space like the Zero Virus did in the X Series, that can't be a coincidence. The Zero we play as in the Mega Man Zero Series is the original mind of Zero that Wily created but with none of the Viral Programming that made him the Maverick that Sigma encountered. From this point of view Omega is Zero in the sense that he is the original Viral Program that Wily intended to release upon the world, but our protagonist is also Zero because he is the same one we played as in the X Series. Neither is a copy as far as the mind is concerned, both Zeroes are pieces of each other. Zero's eventual defeat over Omega Zero in every sense of the word purges him of the past, the horror of the virus that had caused all the wars he had fought and Wily's legacy were all personified in the foe before him.
 * Left open to interpretation. In official commentary for the Zero series Makoto Yabe (Scenario Writer) and Ryota Ito (Series Director) have a discussion about the nature of Omega's origins. Makoto Yabe explains that Omega's personality was certainly programmed by Weil to be his personal messiah that would help him rule the world, but expresses doubt that Weil created Omega's mind. Ryota Ito then chimes in by saying that the original story board idea for Omega was that Zero's original body still contained the Maverick programming created by "a certain doctor who has tried to take over the world innumerable times before" (obviously Wily), and that said side of Zero's personality took over control of the original body once Zero's mind was removed from it. However he states that since they don't discuss the issue in the actual game itself the fans are welcome to come to whatever conclusion they want to.

Zero knew all along about the connection between the guardians and X.
Only subconsciously though. Explains why they are the only antagonists that Zero never kills throughout the series (Phantom killed himself). Zero sensed the connection between them and X, thus when confronted with them, Zero chose to drive them off rather than destroy them. Even when Harpuia was pleading for Zero to Mercy Kill him, Zero sought to save him.
 * When facing Copy X Zero tells him that while the majority of his memories of the past are gone he seems to remember that the original X was much stronger than his Copy is. He also praises the original X as someone who was his friend and whom he knows was much more noble than the current reploid in front of him who has taken on his name. I would say it is certainly plausible that Zero has a sense that the Guardians are similar to X and only fought them because they were in his way, for example back in Mega Man X 5 Zero fought X even though he considered him his best friend.

Zero was a Maverick the whole time
And not in the corrupt Neo Arcadia Distopia style of twisting the usage of the word to persecute innocent reploids either, in "the bad ending of X5" way. Ciel is Dr. Wily's great great (ect) grand daughter and when she discovered ancient blue prints of his master creation she decided to seek it out. Zero's mind is so distorted though that he sees pure evil as good, and honest benevolence as something to destroy. Thus Neo Arcadia actually IS a utopia, the X we all know and love is in charge and is greatly pained to see his long lost friend has resurfaced as a mindless killing machine used as a mere weapon by the descendent of his forebears nemesis. This of course means the Cyber Elf X that Zero knows is actually the Obi-wan style AI ghost of Dr. Wily the same way Dr. Light was for X in his series. And Dr. Wile, Complete Monster extraordinaire, is actually a Dr. Light spirit infused robot body that is created in desperation to bring back X when he was first destroyed, which is why from Zero's perspective he seems to irredeemably evil: because in his twisted Maverick mind the ultimate figure of good is the type of person who gleefully skips across the Moral Event Horizon. Of course even this act of pure desperation isn't enough, and in the end X destroys himself after being defeated by his friend again rather then endure more senseless fighting. Unfortunately this drives Dr. Light into desperation to bring back the original Zero body, and again since our Zero sees it as a mindless figure of unending destruction, in reality Omega probably was the closest thing to our old Zero that we knew and loved. This would also mean the 4 Guardians were originally stalwart figures of peace, but secretly resented being built for combat and never having a war to fight outside of poultry Maverick outbreaks, so when Zero was awakened they found true meaning in combat and ultimately turned against their master though never sinking so low as to side with that vile spawn of Wily we know as Ciel. And Elpizo was probably this series equivalent of Dr. Doppler in X 3 or something. Obviously this theory implies copious amounts of Brainwashed and Crazy (of a sort) "I Know You're in There Somewhere" Fight s against X, the good guys having to choose the Lesser of Two Evils in their fight against the Red God of Destruction Wily created by turning Neo Arcadia into a strict police state to protect its citizens which leads to Zero 4, and in the end an obvious The Bad Guy Wins and You Have Outlived Your Usefulness closing of the series.

When they punished Weil, they mutilated his body.
To prevent him killing himself. Granted Weil has proven himself to be extremely egotistical, and may think he shouldn't kill himself "until they suffer", but after enough time, he'd just give up. To prevent this, they made sure he couldn't get out of his bio-suit: by wrecking his body to the point it doesn't have the strength to break out. Weil ended up losing everything below his diaphram, and the majority of his muscles and flesh.

The reason why he hasn't/didn't starve/bleed/die from shock is due to the orange liquid. It cauterizes all wounds, and functions as an anasthetic(of course, he'd still suffer from the psychological pain). Cybernetics would get rid of the toxins, and generate energy to keep the body from starving/suffocating. The suit would be desinged to prevent it from injuring itself, so the metallic limbs can't rip it apart. His tounge was also cut out and replaced by a mechanised one. to prevent him from biting it off to bleed. No wonder Weil was so pissed: He's a mutilated, living corpse unable to eat or breath. Unable to feel anything. Forever.
 * I dunno about that; in Zero 4 he once got his glass helmet cracked out (after he got a direct hit from Ragnarok's laser and later after his first form boss fight), but he still managed to stay alive.
 * Like I said, everything below the diaphram, meaning that his lungs are still able to inhale and exhale. Plus they'd be smart enough to prevent liquid getting out of his chest region, so it would presumably shut off when the helmet is broken. That, or the cybernetics have a breathing supply for him. How else would you explain him not asphyxiating before going One-Winged Angel, considering the final stage had the vacuum of space and the Earth as a backdrop?

Zero was really Ciel the whole time.
Ever wondered how Zero and Ciel look so much alike? Or how Ciel was able to create the biometals without Zero's body? Or how Zero's memories are sketchy at best?

Because Zero never woke up that day. Only Ciel thought he did.

To be fair, having your closest friends die off one by one in your face an take a toll on a person, and by that point death was staring her down. So, instead of Passy waking Zero with a slim chance of working, she altered Ciel's mind and a nearby Power Suit to cope with the circumstances, creating a Split Personality. When she came back to resistance base, everybody else just played along, adding another PTSD victim to the madhouse.

But she started winning battles.

Since all records of the Elf Wars were classified, Neo Arcadia took Ciel by her word that she was Zero. Even X himself, broken beyond belief his friend went maverick in the Elf Wars, played along because he was desperate.

Thus, in Z2, when Zero was stranded out there? Either Ciel thought he escaped somewhere else when she was teleported, or Ciel's Power Suit was strong enough for atmospheric reentry and Cerveau took over while she was gone. In Z3? Omega could've been a Shape Shifter all along like the newer generation reploids. In Z4? Ciel managed to escape via transport, but she feel into a trance imagining Zero was still fighting Weil.
 * Then what about the beginning of Z4, where Neige speaks to both Ciel and Zero at the same time and welcomes Ciel while telling Zero to shove off? Schizophrenia for everybody?

Due to Copy X's nature, he was doomed to go crazy
When Copy X finally meets Zero, he freely admits that he is a copy of the original. But how exactly did he come to this conclusion? Everyone believed him to be the true X, except for Ciel. Imagine how his life would have been ever since he was born; he's activated as a newborn reploid with the experience of a child, but everyone around him believes that he's their beloved X come back to them. Already he's had an impossibly heavy mantle of expectations hefted onto his shoulders before he even really knows what's going on. So he tries to fit into these large shoes and be the 'X' they want him to be - after all, they say he's X, so he must be X, right? But ... he doesn't have any of the memories or experiences of the original X. Eventually he comes to the only real conclusion; that he's only a copy of the original. His entire life is based on a gigantic lie. If everyone knew the truth they would abandon him, because he's not the X that everyone loved and respected. He, understandably, suffers a psychotic break. It's at this point that he begins his campaign of iron-fisted rule, because if he can't be the beloved X, then he has no choice but to be better than him in order to earn that love by his own merits. Copy X might be a cruel tyrant, but his upbringing really didn't leave any room for anything but an unstable, emotionally skewed indiviudal.