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Hijacked by Sigma?!?

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 wanted 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.
    • X was a prominent public figure (even if just his copy). So much so that Elpizo and every Reploid you meet in the entire series could well be justified in saying that they had "known" X their entire lives. Mega Man X, the ruler of Neo Arcadia and most powerful known reploid, would give cause to anyone to shout "at last." After all, Elpizo had been part of the resistance fighting X.

The Four Guardians have the hots for Zero... and so does X.
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:
    You know, X has many Ho Yay moments with Zero in the X series. And then the Four Guardians are created, using X's DNA as a base. As a result, three of them love fighting Zero. Leviathan got the dominant homogeneous allele, 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.
    • 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. Explanation 
    • 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.
      • Memory can play a part in shaping souls. If the manga is to be believed, then Leviathan is the part of X's soul that consists of his memories about Marti. Think about it, both are aquatic reploids who wield a polearm and love to tease the main characters.
      • 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. According to the MMZ wikia, Leviathan doesn't particularly enjoy violence that much, but she thoroughly 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 adequately 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...

The "Elf" in Cyber-Elf is an abbreviation
For "Electronic Life Form" or "Energy Life Form".
  • That's called an acronym.

This happened one of 3 waysPersonally I think one of 3 things happened

1) He was the first victim of the Elf Wars. Weil decides not to attack X or Zero first, the former being the strongest hero at that point, and being likely heavily guarded by the 4 Guardians or other loyal subordinates, and the latter likely being heavily guarded himself since a released Maverick Virus, or even worse, maverick Zero, is a top-priority threat. So, he went after the strongest hero besides those two (Although I'd place Harpuia as stronger than Axl, personally) as a "test run" of his mobile WMDs. Axl gets wind and tries to warn X, but was killed by Dark Elf and/or Omega (Or even possibly by Weil himself) before he could do so, leaving Weil still with good publicity.

2) Axl was the quaternary antagonist of the Elf Wars (After Weil, Omega and Dark Elf), being controlled by Dark Elf. He's eventually put down by X before Zero joins in, having been too far gone to turn back to reason, and the catalyst for X's near Despair Event Horizon.

3) Ciel sought out Axl first since they knew where he was, and told him everything about the sick dealings of Neo Arcadia. He joins the resistance and is their best guy as they don't know where Zero is at that point or even if he could be activated. Eventually, Axl is killed either by Harpuia sparking his Character Development or Copy X. This drives them to find Zero as they have no other choice at that point.

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 succeeded.

Weil wasn't always evil.
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 becoming Mavericks. Sounds like a good idea, right? note  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 submit to the humans' will. To sum it up, he was a Well-Intentioned Extremist (heck, his methods weren't that extreme), but then he crossed the Moral Event Horizon by creating the war in the first place.

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. 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 successfully 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 storyboard 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.
    • It makes sense. Omega acts like how "Zero" did when Sigma first found/fought him in the ruins of Dr. Wily's lab. (And even more so like Awakened Zero). The "Zero" we most know from the X series games is a personality that somehow developed after Sigma knocked him out in that fight (after that W appeared on his head jewel and caused him disabiling amounts of pain). So, essentially, Omega IS the original personality. Zero, through the X games, was a personality that hijacked Omega's body. Dr. Weil gave Omega a factory reset and then changed his loyalty from Dr. Wily to himself (given his similarities to Dr. Wily, even in name, this probably was not hard for him to achieve). So, in this sense, Zero (upon awaking in MMZ 1) isn't a copy, but himself given his own body for the first time, even if the body itself is a imperfect copy of Omega's. The final battle not being "Zero" (in a copy of his own body) vs "Omega (who had stolen his original body), but just Zero (the new personality in a body that is truly his own) vs Omega (the original personality in the original body).

There are actually three Zero personalities .
In the X series, Zero had two sides: The Zero that fights for the Maverick Hunters and The Zero that infected. However there's a third personality: the mindless loyal soldier. Let's call them Zero, 0 and Omicron respectively. Originally, Zero was meant to be a combination of Zero and Omicron, however a defect in his program led to 0 being dominant. Thanks to Sigma, Zero became the dominant personality. After Zero entered a clone body, Dr Weil felt this was the perfect opportunity to have Omnicron the main personality...however while dominant, the 0 personality was still there and influenced Omicron, resulting in Omega: a God of Destruction with the insane soul of 0 and the loyal mind of Omicron. [[Sadist|Being Dr Weil]], this was a great combination and led to the Elf Wars.

  • An alternative intepretation of this WMG: Zero's third personality is the original identity under the Virus that was designed to control him, the one that angered Wily with his rebellious (and possibly heroic) ways and was sealed in a capsule for XX years while the Virus assumed total control of him. It ends up becoming his "true" dominant personality later after Sigma freed him from the influence of the Virus before the events of the first X game, and survived transference into his 'copy' body that he uses for the entire Zero series. It is entirely possible fragments of this true personality remain inside his original Omega body, thus allowing for his true resurrection in the distant future.

Zero knew all along about the connection between the guardians and X.
Only subconsciously, though. It 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 X5, 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 Dystopia style of twisting the usage of the word to persecute innocent reploids either, but in "the bad ending of X5" way. Ciel is Dr. Wily's great great (etc) grand daughter, and when she discovered ancient blueprints 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 he is greatly pained to see his long-lost friend has resurfaced as a mindless killing machine used as a mere weapon by the descendant of his forebear's 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 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 be 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. The real Weil had simply been executed for his crimes. 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 than 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 X3 or something. Obviously, this theory implies copious amounts of Brain Washed 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.
  • I won't delve into some of the details proposed here (because I don't agree with them and it should be left at that). However, the basic premise is true: Zero is a Maverick, and always was a Maverick. He just doesn't like to be the reason for destruction and deaths, and due to being built like that from the very beginning (as opposed to becoming a Maverick as a result of the virus' effect) he has enough control to choose not to fight. And it does have to be noted that it is precisely because he is a Maverick that he was able to kill Weil: of the Reploids built before the elf wars, only Mavericks are capable of hurting humans deliberately, so after Weil revealed himself to be a human, a non-Maverick would be stopped from hurting him by their programming.

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 anesthetic (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 designed to prevent it from injuring itself, so the metallic limbs can't rip it apart. His tongue was also cut out and replaced by a mechanized 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 breathe. Unable to feel anything. Forever.

  • I dunno about that; in Zero 4, he got his glass helmet cracked out twice (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 diaphragm, 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?
  • Or better yet, Weil is just a head or a brain in a jar, and his cybernetic body has programming within it that keeps him from committing suicide. If this picture is anything to go by, even most of his head is robotic.
  • Then again he mentioned that they digitize his mind so that he'll forever reflect on his sins; At this point he's no longer human, he might as well became a Maverick that needed to be put down. And even then, it won't do him any good as his consciousness live on through Model W in the ZX series.

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 can 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 Shapeshifter all along like the newer generation reploids. In Z4? Ciel managed to escape via transport, but she fell 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?

The Green Biker Dude is Harpuia.
Why the hell not?
  • Well, Harpuia is supposed to be the smartest of the four guardians. Running your bike into oncoming fire, resulting in his untimely demise, didn't seem like a good idea.
  • Then again, this is the same Harpuia that thought that staring down Omega when it melded with the Dark Elf, giving him enough time to throw several orbs at him, was a good idea.
    • Be fair, that lightning attack Harpuia used can tear shit up if he manages to hit you with it.

Weil modified Zero's body before he gave it the external armor and installed a new personality
That would explain how Omega's true form looked somewhat differently than Zero's body design we saw in the X series. Zero's new constructed body (that was then used to battle Omega) is likely based on this new design, to match.

Ciel is an expy of Iris
They both have a pacifistic personality, an attraction to Zero, and a familial relationship (of sorts) with a reploid Zero is antagonistic towards. They even have similar haircuts! In fact, you could argue that the resistance as a whole is an expy of Repliforce (falsely accused of being Mavericks, fondness for berets).
  • They're more like a Repliforce that wasn't guilty of all sorts of ancillary crimes. Let's face it, Repliforce wasn't an innocent puppy. When a military organization is implicated in a major atrocity, refusing to disarm and come in for questioning is the kind of thing that should send up warning signals.
    • The only thing Repliforce was guilty of was not offering themselves on the chopping block for a crime they didn't commit. The above entries on this very page about the actions of humans in the Zero series makes it a very reasonable point of view on why Repliforce wouldn't trust humans to give them an impartial trial, what was most likely was going to happen if they had peacefully disarmed would be humanity retiring them all without bothering to get proof of them being part of the crime.
      • Then maybe they should have made that argument, because when a group of heavily armed soldiers who stand accused of (and have witnesses testifying to) destroying an entire city respond to the very reasonable request of coming in for questioning by spouting questionable military philosophy and the flowery military prose equivalent of "you can take our guns when you pry them from our cold dead fingers", one doubts any army in that situation, reploid or human, would be allowed to continue to exist after that. Furthermore, considering that the Zero series happened after over a century of Reploids going on murderous rampages or doing boneheaded stupid things for entirely self-serving reasons, it's probably just as valid to assume that instead of the Zero series being proof that Reploids prior to that era wouldn't be given a chance, but rather not giving Reploids a chance was learned through hard, bloody experience. And considering that Storm Owl proceeded to terrorize the skies and Jet Stingray destroyed a different city, Repliforce doesn't exactly strike me as the kind to try and help their case. For cripes' sake, you're declared Maverick because people think you destroyed a city, and you respond by destroying another city?!?!?
  • Arguably the Resistance is even worse than Repliforce because they are a group of Reploids openly defying humanity from the beginning. They raid supplies, assault Neo-Arcadian bases, were behind the assassination of Megaman X, and a year later in the case of Elpizo's "Operation Righteous Strike" they attacked a residential area full of civilians as part of an attempted invasion force. The Resistance did the exact same actions that Repliforce did, they refused to surrender themselves, took over territory that didn't belong to them, attacked the Neo-Arcadian Maverick Hunters, and even threatened civilians. The fact that Ceil is their token human doesn't change the fact that they are a group of Reploids fighting against the government of Humanity. They are in every sense of the word Mavericks, only they don't have Sigma manipulating them.
    • This would make them closer to the Rebellion, except unlike either, their actions weren’t as destructive. And Neo-Arcadia themselves become Maverick by Zero 4.

Cyber-Elves are based on virus technology.
They perform similar functions, potentially altering Reploids. However, this is not a bad thing. Gene therapy uses viruses as vectors, so they might use Cyber-Elves in a similar manner.
  • As Mother Elf was derived from Zero's residual viral readings - a vaccine, so to speak - it's possible that regular elves are similar in nature.

Zero's appearance is due to constantly evolving technology.

When this series first started, a lot of people commented about Zero's new appearance. Capcom gave a rather flimsy explanation for this, stating that this was how Zero always looked, and it's just the art style that makes him appear "different".

However, I have a better theory about this, because I absolutely refuse to accept that as an answer.

If we observe the designs of the main characters in Mega Man X8, they've been slimmed down considerably, from bulkier, heavier frames to more agile, lightweight models. As we can observe from devices that we use in our lives (such as television sets, personal computers, and MP3 players), technology tends to lean towards being more convenient and 'compact' as it evolves. There's no reason not to believe that by the time of Mega Man Zero, the overall designs for reploids eventually did away with the bulky armor and lent themselves towards more human designs.

With that said, as technology progressed, there's no reason not to believe that as Zero's body was worked on, it would have gone through systematic updates and upgrades in the process, to keep up with modern technology. Weil most likely did the same with Omega (Zero's real body), following similar schematics for Zero's duplicate body, as he needed it for more active use during the Elf Wars.

That is why neither Zero nor Omega "look" they way they should — they've been altered to keep up with the times.

  • The Archie Comics continuity, at the very least, seems to implicitly favor this interpretation, using any version of the characters depicted wherever they should be used; X1 Zero in any event set before X1, post-X2 Zero in any X Series event after he was rebuilt, Zero Series Zero (and Zero Series everyone else, for that matter) in a vision Dr. Light had that predicted the Zero Series events, among other things. With no sign of one appearance overriding the others, the comic's take on it makes it at least semi-canon.

X used to have Copy X's angelic armor and One-Winged Angel

First off, the Dark Elf has the ability to transform any robot into a stronger and then monstrous form of itself. Look no further than Elpizo or Omega, for instance. The Dark Elf used to be the Mother Elf, and the manual stated that X used Mother Elf to purge the rest of the Sigma Virus on earth.

Now, onto the theory: the Mother Elf modified X's Ultimate Armornote  and gave it a white and gold color instead of the black and purple one. It also later gave him a seraphic form that was likely to be used only once. After that X became widely known for having that form.

When X went missing to seal the Dark Elf within his inactive body, the "Savior X" later became the template for making Copy X, complete with the extra forms above but without influence from the Mother Elf; this also hypothetically makes Copy X's forms weaker than X's.

Consider the following:
  • Copy X was originally going to be X himself.
  • Mega Man X5 was supposed to be the last Megaman X game.
  • X5 hints that Dr. Wily is still alive.

See where we're going with this? Wily was most likely supposed to be the real Big Bad of Zero, but for whatever reason, he was replaced by Suspiciously Similar Substitute Weil. Which is to bad, as it would have made Zero 3 and Zero 4 more epic. Omega would be played up as how Wily wanted Zero to be, and at the end Zero would sacrifice himself to defeat his creator.

And then Wily becomes Model W in Mega Man ZX.

After Zero dies, he goes to Cyberspace and hangs out with X and the Four Guardians.
Because Zero deserves a goddamn break after everything he's been through.
The Four Guardians' personalities are all based on aspects of X
While they were just born from his DNA, their personalities quite match as well.
  • Harpuia: X's sense of justice and desire of coexistence with humanity.
  • Fefnir: X's power and determination. Note that without X's pacifism to temper it, Fefnir becomes a Blood Knight.
  • Leviathan: X's more naive side, brought to a new level.
  • Phantom: X's loyalty to duty.

Zero's original body already had Element Chips built-in, but the reproduction body doesn't have them for some reason.
Think about it; many of Zero's original Command Arts had the same elemental properties as the Element Chips he has to re-collect in his reproduction body every Zero game. There were several Ice-element Command Artsnote , several Fire-element Command Artsnote , and several Thunder/Lightning-element Command Artsnote  among many other elemental attacks throughout his X series history that, unlike the first three elements, cannot be acquired at all in the Zero series. Why does he suddenly need to collect element chips to imbue his attacks with said elements again, including certain EX Skills that look suspiciously like some of his old Command Artsnote ? Because his new body can't do that by default. Whoever built it left some pieces out.note 

Dr Weil's cybernetic suit was a Flawed Prototype in an attempt to achieve immortality.
Seems odd they would go out of their way to invent a means of immortality just to punish Doctor Weil, so it's likely it was already around for beneficial purposes. Developed in the 22nd/23rd century, his suit was originally an attempt to give people the immortality the human race had dreamed of for millennia. The orange fluid would retard aging, heal wounds, prevent illness/infection and possible give nutrients. Weil is at least machine from the chest and possibly even just a head in a jar because the removed organs decay over time, and needed bionics to last indefinitely. Weil's modified ability to never forget is to prevent the brain from decaying over time. Initially it would be used to save people's lives and achieve eternal life.

However there were many things that made the suit a Fate Worse than Death; being unable to taste, touch or naturally sense the outside world, still aging in a way (Weil looks pretty ghoulish, and we don't know whether he was old when he got into the suit or if he was a lot younger than he now looks) and the orange fluid must feel really weird. Noticing this, they gave up on it. Only when Weil dwarfed Adolf Hitler and Genghis Khan combined in mass death did they decide to use it, this time as a means of inflicting the ultimate punishment.

Dr Weil is Ciel's ancestor as well.
He was working with her ancestress that created the Mother Elf. He would've been significantly less Obviously Evil at the time, and if they were married it might explain how he was able to hijack the project. Obviously after the Elf Wars this fact was hidden or not spoken about, and Ciel is in no rush to reveal that she's related to the Hitler of that era. She inherited his genius along with her ancestress.

The Zero takes down his opponents as quickly as he would in a TAS speedrun.
Because those are awesome and so is he.

He's already old in the Elf Wars, and it's implied that and the X series were several decades off. Either his parents were on Sky Lagoon when it was crashed, or died in the crossfire of the Repliforce and Maverick Hunters fighting. That's why he hated Reploids so much and thinks they shouldn't have free will-he suffered in one of the conflicts that involved Reploids not caused by the Maverick Virus, nor a group of obvious renegades, but two forces meant to keep the peace. It's why he never thought eliminating the virus went far enough. However decades of resentment, as well as further, similar conflicts (The Maverick Hunters exterminating the works of Gate, Maverick Hunters Vs. Red Alert, Maverick Hunters Vs. The Rebellion and probably countless off-screen conflicts) caused him to jump the slippery slope and the idea of controlling Reploids became too attractive an idea to pass up, abandoning any good intentions he originally had to Take Over the World instead.

The Copy X in Mega Man Zero is the second Copy X to exist.
The first one worked perfectly, but was destroyed when he spontaneously exploded by accidentally touching one of the spikes in Neo Arcadia Tower when the Trans Server was down for maintenance. Ciel made a copy of him, thereby recreating the duplication of X.

X's final piece of dialogue in Z1 went completely unchanged when they gave X's role to Copy X
(Zero defeats X's final form)

X (From Copy X's Dialogue): "How can this be... possible... I was supposed to be... a hero..."

Zero (approximation): "I've just remembered something... You fought for peace between humans and reploids. That's what made you a hero"

X: "Since you disappeared I've been fighting this war alone against an uncountable number of Mavericks for nearly a hundred years... Battle after battle... So painful and so sad... But the hardest part was when I discovered that I no longer cared about fighting enemies... I'll leave this world to you... Please allow me... to rest in peace... for a while............I'm sorry, Zero..."

Zero: "So be it... But that's why we are the best partners... I'll do what you want... Rest for a while. I will handle it, you can count on me. I won't stop! When an enemy appears... I'll terminate it..."

Neo-Arcadia is located in France, Quebec, or some other French-Speaking region.
Hence why all the humans' names (minus Weil, as he predates Neo-Arcadia) are French (Ciel named the Reploids in the Resistance, hence why all their names are French as well).

Zero obtained his replica body in the X Series
Prior to the Elf Wars, Zero had a replica body. In Megaman X5, Zero’s body had become damaged to the point he “died”. Of course, Zero does get better after a few years in-universe, meaning somewhere along the way, his original damaged body was switched out for a reproduction, and he was never aware of it. The evidence of the argument also points to Weil possibly being the creator of Zero’s replica body.

Omega is Dr Weil's attempt to finish what Wily started.
Dr Wily's strategy in many of the classic Mega Man games is to reprogram/mind-control other robots to do his bidding. Supplementary material has it that Zero wasn't properly finished, having a cognitive flaw that made him unstable and violent, and the virus present in him spread that and warped those who it infected. And from the likes of Sigma's usage we known that the Maverick Virus can be used as a form of control. Now look at Omega; he has Zero's original body, and while Ax-Crazy is as obedient to Weil as Zero should've been to Wily. And it conjunction with the Mother Elf, is capable of mind controlling Reploids en masse. Could this be an insight on what a "completed" Zero would be like? Wily's hope was that a subservient Zero would use The Virus to mass-brainwash other robots, to serve as a swift take-over as even a super-fighting robot couldn't accomplish it alone. Dr Weil, being an Evil Genius who knows his history and had his hands on Zero's original body, figured this was the plan of Dr Wily and decided to copy that plan. Being that he worked with Ciel's ancestor who made the Mother Elf, he could've incorporated that as part of her design...though he had to steal her and "upgrade" the Mother Elf to the Dark Elf for it to work.

Dr Weil is subconsciously goading Zero to kill him.
He does consider his immortality a curse. While his Pride and sadism boasts he'd survive the crash and wants to see human and Reploid forever squirm, deep down he wants to die and uses the Villain Ball of a warning shot in order to goad Zero to come finish him off. If it takes down Zero, and the last place on Earth anyone could live on now that Craft has wrecked Neo Arcadia, it's all the better. Unfortunately for Weil not only does he fail to take anyone outside of Zero, but he's still alive in the form of Biometal W.


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