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 (including ones acting 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, for example, would be charged not as Mavericks, but as criminals. As X8 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 Repoids should pay for what Sigma and the other Mavericks did — the ones who've 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.
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 Fafnir dick around waiting to play with 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 BastardBig 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.