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1* The incident that started the series was made of this. After decades of research, the scientists of Neo Arcadia have finally managed to create the ultimate vaccine to the Sigma Virus thanks to their studies of Zero. The government has effectively cured every viral Maverick on the planet, but also plan to clear ''every'' Maverick--even those without the influence of the Virus--of all charges. This does not sit well with Dr. Weil.\
2'''You'd expect''': He'd appeal to his superiors that the Mavericks who could reasonably be said to have acted of their own free will, such as Dynamo, would be charged not as Mavericks, but as ''criminals''. As ''X8'' [[ContinuitySnarl later shows]], the two are (or are ''supposed'' to be) separate classifications. As for the former Mavericks, he could simply suggest surveillance measures be put in place, for safety's sake. After all, this wouldn't be [[VideoGame/MegaManX3 the first time]] a so-called vaccine turned out to be a placebo.\
3'''Instead''': He decides ''all'' Reploids should pay for what Sigma and the other Mavericks did -- those who have been cured, innocent civilians, and even the Maverick Hunters who fought to protect people from the Mavericks -- and uses the Dark Elf to commit an act of global terrorism. With her and his own personal WMD, Omega, he proceeds to slaughter the majority of the planet's population.
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5* Dr. Weil has just been captured, after cursing the Dark Elf and creating [[OmnicidalManiac Omega]], who has wiped out 60% of the human population and 90% of the Reploid population (This is in the century following the Maverick Wars, including the Eurasia Incident, which already nearly wiped out all life on Earth, meaning Weil followed up a near-mass extinction event with ''another one''). All mostly ForTheEvulz. X, ever the kind soul, spares his life, and instructs his subjects to do the same.\
6'''You'd expect''': His captors would realize that the threat he poses is simply too great, and that [[MoralEventHorizon he is]] thoroughly ''[[ThisIsUnforgivable irredeemable]]'', and [[ScrewTheRulesImDoingWhatsRight kill him, X's orders be damned.]]\
7'''Instead''': They obey X's exact words and punish Weil via a loophole, an escapable FateWorseThanDeath: they seal him in a capsule that prevents aging, but ''keeps'' his memory intact, so he can see how the world thrived despite his actions. Naturally, when some idiot decades later breaks the seal down, he becomes more monstrous and vengeful and eventually succeeds in [[TakeOverTheWorld taking over the world]] and creates a [[CrapsackWorld hell on earth]] to rival the Elf Wars.\
8'''[[JustifiedTrope Justification]]''': [[AllThereInTheManual Supplementary materials]] reveal that [[spoiler:the Eight Gentle Judges presided over his case--Reploids whom ''Weil'' designed. It's quite possible that Weil, predicting the consequences of his actions, secretly programmed them to opt for imprisonment over execution]]. Another possible explanation is that the Reploids ''did'' want to kill Weil, but were too afraid of being branded as Mavericks to go through with it. That being said, this doesn't explain why no ''[[ExactWords humans]]'' [[WhyDontYouJustShootHim killed Weil]].
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10* The Dark Elf is breaking free and X's body is the only thing he knows that can seal it.\
11'''You'd expect''': He'd tell someone what he's doing and set up a successor or a cover story.\
12'''Instead''': He goes away without so much as a word, resulting in the need to replace him, forcing the higher-ups to put a (unintentionally) psychotic KnightTemplar clone in charge.\
13'''Also''': Since few are aware that X is doing this or why, it results in nobody being able to so much as ''try'' to find a way to safely free X from his imprisonment and/or cure the Dark Elf in the meantime.
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15* Elpizo is making headway into the Dark Elf's seal with the Baby Elves in tow.\
16'''You'd expect''': Neo Arcadia would dispatch every available resource, including and especially the Guardians, to intercept Elpizo.\
17'''Instead''': Only Harpuia is sent, while Leviathan and Fefnir dick around waiting to play with Zero.\
18'''Also''': It's implied that the Baby Elves were influencing Leviathan and Fefnir's actions, though now the question is "why didn't they take Elpizo on all at the same time instead of standing guard at each temple and letting him take them out one by one?\
19'''Although''': Earlier on, during Elpizo's 'Operation Righteous Strike', Harpuia, Fefnir and Leviathan beat the entire invasion force and Elpizo without seemingly breaking a sweat. They may have simply under-estimated Elpizo, thinking that he wouldn't be a challenge, even with the Baby Elves.
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21* After Craft seemingly kills Dr. Weil with the Ragnarok Cannon in the fourth game's final levels, the heroes briefly think that everything's done and finished after taking down TheDragon since the cannon seems to have ceased functioning. Except the BigBad is still very much active, and was directly interfaced with and charging the cannon without absolutely anyone noticing.\
22'''You'd expect''': He doesn't let anyone know what he's planning until it's too late, and blows away Area Zero while everyone is too caught up with Craft to figure out his plan. Since the destruction of Area Zero was his plan from the start of the game, [[TheBadGuyWins it would've completed his goals and wiped out the very people Zero fought for in his attempts to force the world into despair.]]\
23'''Instead''': [[VillainBall Weil fires a warning shot just to fuck with the people at Area Zero so they'd flee it.]] Though it is implied he did this on purpose, this results in Zero continuing on to find out what was going on and confront Weil before he can commit to a ColonyDrop on Area Zero.
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25* Craft is dead. Weil is [[spoiler:presumed]] dead. Weil's forces are defeated. Without anybody at the controls, the Ragnarok satellite is no longer firing. Zero is still on Ragnarok, in the main control room in which he had just fought Craft. It came at a considerable cost to all involved, but it seems that our heroes may have won the day.\
26'''You'd Think:''' Zero would make sure Ragnarok can't be fired again or {{Colony Drop}}ped on anything important before transferring back to Earth. He's in the main control room, he's already disabled the cybersecurity keeping the Resistance from hacking the satellite, and most of Earth is unpopulated wasteland. From this position, disposing of the satellite wouldn't have taken much effort, barring any unforeseen surprises Weil left behind.\
27'''Instead:''' Zero just transfers out, leaving a fully-operational KillSat in orbit with the keys still in the ignition. He gets the chance later to follow through on destroying Ragnarok, but circumstances by then have driven the cost [[HeroicSacrifice significantly higher.]]
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29* Zero finally meets Dr. Weil face-to-face after the above events, and commit to their final showdown.\
30'''You'd expect''': Weil knows damn well that Zero is a force to be reckoned with given the countless numbers of foes he's cut down regardless of the odds (not to mention purifying the Dark Elf ''and'' destroying Omega, two things X and Zero weren't able to do together a hundred years previous), and should immediately do ''everything'' within his immense power to kill the robot with whatever he's got. He also has a regenerative, nigh-immortal body that would allow him to stall for time as Ragnarok continues its descending course, as it's allowed him to survive his imposed exile to the hellish wastelands outside Neo Arcadia for a century already.\
31'''Instead''': He directly fights Zero, which doesn't go according to plan and causes him to get struck down momentarily.\
32'''And Then''': This causes Weil to fuse himself with the core of Ragnarok in a fit of megalomania and then [[TemptingFate dares him to cut down a human]] out of a moment of being a contemptuous, [[FantasticRacism racist]] prick over the ThreeLawsCompliant concept (that Zero and Reploids in general do not follow) in a last-ditch attempt to complete his ColonyDrop plan.\

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