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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.
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.
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.
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 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.
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.
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.
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