- 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.
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 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 the first time a so-called vaccine turned out to be a placebo.
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.
- Dr. Weil has just been captured, after cursing the Dark Elf and creating 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 For the Evulz. X, ever the kind soul, spares his life, and instructs his subjects to do the same.
You'd expect: His captors would realize that the threat he poses is simply too great, and that he is thoroughly irredeemable, and kill him, X's orders be damned.
Instead: They obey X's exact words and punish Weil via a loophole, an escapable Fate Worse than Death: 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 taking over the world and creates a hell on earth to rival the Elf Wars.
Justification: Supplementary materials reveal that 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 humans killed Weil.
- The Dark Elf is breaking free and X's body is the only thing he knows that can seal it.
You'd expect: He'd tell someone what he's doing and set up a successor or a cover story.
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 Knight Templar clone in charge.
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.
- Elpizo is making headway into the Dark Elf's seal with the Baby Elves in tow.
You'd expect: Neo Arcadia would dispatch every available resource, including and especially the Guardians, to intercept Elpizo.
Instead: Only Harpuia is sent, while Leviathan and Fefnir dick around waiting to play with Zero.
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?
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.
- 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 The Dragon since the cannon seems to have ceased functioning. Except the Big Bad is still very much active, and was directly interfaced with and charging the cannon without absolutely anyone noticing.
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, it would've completed his goals and wiped out the very people Zero fought for in his attempts to force the world into despair.
Instead: 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 Colony Drop on Area Zero.
- Craft is dead. Weil is 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.
You'd Think: Zero would make sure Ragnarok gets destroyed — or at least disabled beyond all capacity of ever being fired again — before transferring back to Earth. Death Is Cheap for a Magnificent Bastard Big Bad in a Mega Man game, and Zero's seen Dr. Wily team up with Sigma to torment him despite being long-dead. Even if Dr. Weil really is dead, Zero has no idea how many Brainwashed and Crazy followers he still has left.
Instead: Zero just transfers out, leaving a fully-operational Kill Sat in orbit with the keys still in the ignition. He gets the chance to follow through on destroying Ragnarok after Weil's moment above, but Weil's escalating efforts to destroy Area Zero in spite of Zero's efforts to stop him drive the cost significantly higher.
- Zero finally meets Dr. Weil face-to-face after the above events, and commit to their final showdown.
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.
Instead: He directly fights Zero, which doesn't go according to plan and causes him to get struck down momentarily.
And Then: This causes Weil to fuse himself with the core of Ragnarok in a fit of megalomania and then dares him to cut down a human out of a moment of being a contemptuous, racist prick over the Three Laws-Compliant concept (that Zero and Reploids in general do not follow) in a last-ditch attempt to complete his Colony Drop plan.
Result: He fails, as this lets Zero directly destroy the core and finally kill Weil simultaneously. While this succeeds in killing Zero, it also results in Ragnarok breaking up in the atmosphere before it can harm anything and Weil himself effectively trapped in the pieces of ruins and debris out of the sheer fact that he absolutely underestimated Zero. Yet again. About the only justification Weil has for being this thoughtlessly reckless is that he's a potential Death Seeker aiming to escape his immortality, but he still ruined his plans near-entirely.
What An Idiot / Mega Man Zero