* Zero's decision to kill Weil seems to be spitting on the laws of robotics that were so important to the series. However, his decision is in accordance to the Zeroth Law of Robotics which in essence is a threshold law designed to protect the human race, as obeying law 1 would cause humanity to be harmed through inaction. It's made especially ironic given that Zero was never built with the laws in mind (Wily made him and all, and he's technically a "Robot Master"), yet he unwittingly follows the most important law.
** Also: ''[[MeaningfulName Zer]][[PunnyName oth]]'' Law.
*** Weil is also a mass murderer despot. The sprirt of Law Zero was intended specifically to stop people like him (think of Adolf Hitler and Pol Pot), and will override the first law.
*** All of this comes up because Weil himself brings up the topic, that Reploids like Zero should serve, and never harm, humanity. It basically blows on Weil's face due to the Zeroth Law.
*** Also, Dr. Light's dream was for humans and robots to live and treat each other as equals. Zero treated Weil like any other Reploid he's fought, demonstrating that equality. He even outright calls him "just another Maverick," a term which up until the fourth game was [[FantasticRacism used exclusively for Reploids]]. This also explains why it fell to Zero to realize Light's dream: for all his talk, Light subconsciously ''did'' still put human life higher than robots, hence Rock being ThreeLawsCompliant and X's 30 years of testing. If he had accepted that there are times to kill, Dr. Wily would've been picked off before Zero could be built, preventing so much pain and suffering.
*** Speaking of which, remember the ending of ''VideoGame/MegaMan7''? Wily got away because Mega Man couldn't follow the Zeroth law. Then he went on to create the Maverick Virus, and you know the rest. By following the Zeroth Law, Zero was able to do what Mega Man could not -- destroy the villain and create an era of peace.
* The final battle with Zero and Omega Zero can mirror the fact that Zero is fighting his [[SuperPoweredEvilSide old self]]. Remember that in ''X2'', Sigma made reference to Dr. Wily for Zero being his last creation made. In ''X4'', we know who the silhouette is in the beginning of Zero's nightmare. And ''X5'', everyone obviously knows, but Sigma does not refer to him by name to X and Zero. Also, Zero was ''AxCrazy'' with Sigma's flashback. All the plot build-up from the entire ''X'' series to ''Zero 3'" makes a true resolution of the story of Zero finally taking down what represented his evil side. And since Zero lost his original body, Dr. Wily's final creation is technically destroyed, but the original Zero's mind still exists.
* Why doesn't X show up in ''Zero 4''? He's finally dead. In ''Zero 2'', his physical body's destroyed, and in ''Zero 3'', he leaves Zero to return to Cyberspace.
* The [[NoExportForYou Japan-exlcusive]] e-Reader cards also appearing in the CompilationRerelease on the DS (this time in all regions) includes a poster of [[VideoGame/MegaManBattleNetwork [=MegaMan.EXE=]]] alongside a poster of Ciel. It may seem a bit of a stretch, but both of these series were released around the same time and were the first two series to finish their storylines. Another thing they have in common: Cyberspace!
** By extension, the [[BlindIdiotTranslation Z-Saver]] chip in the Battle Network series features Zero series Zero through the same connection.
** This may count as Fridge Heartwarming: At the end of the series, Zero is dead and is supposedly in Cyberspace. Fastforward to VideoGame/ProjectXZone, Iris is brought back thanks to the representatives of Franchise/DotHack. Now, what does .hack have in common with the Mega Man series? Cyberspace. Zero also vows to find Iris once again. So, in essence, at the end of the series, Zero and Iris are finally [[TogetherInDeath reunited]].
* In the manga adaptation of the first game, Copy-X (here called the "Perfect Reploid") is a fusion of the Four Guardians created by [[CanonForeigner Ciel's younger sister, Cial]], rather than a copy of X himself. It may sound crazy, but the Four Guardians were made from four pars of X's [=DNA=] in the series.
* Of course the Proto Form[=/=]Junk Armor would reduce your defense. WordOfGod says it's the Black Zero armor from the X games. Where does Black Zero appear the first time? At the end of ''X2'', when it was easily destroyed with a single slash.
* Due to Copy X's nature, he was doomed to go crazy. When Copy X finally meets Zero, he freely admits that he is a copy of the original. But how exactly did he come to this conclusion? ''Everyone'' believed him to be the true X, except for Ciel. Imagine how his life would have been ever since he was born; he's activated as a newborn reploid with the experience of a child, but everyone around him believes that he's their beloved X come back to them. Already, he's had an impossibly heavy mantle of expectations hefted onto his shoulders before he even really knows what's going on. So he tries to fit into these large shoes and be the 'X' they want him to be -- after all, they say he's X, so he ''must'' be X, right? But... he doesn't have any of the memories or experiences of the original X. Eventually, he comes to the only real conclusion; that he's only a copy of the original. His entire life is based on a gigantic lie. If everyone knew the truth, they would abandon him, because he's not the X that everyone loved and respected. He, understandably, suffers a psychotic break. It's at this point that he begins his campaign of iron-fisted rule, because if he can't ''be'' the beloved X, then he has no choice but to be ''better'' than him in order to earn that love by his own merits. Copy X might be a cruel tyrant, but his upbringing really didn't leave any room for anything but an unstable, emotionally skewed individual.
** Bonus: he ''wasn't'' put into 30 years of morality testing, unlike X. He really doesn't know better about the right thing to do.

* Omega, the AxCrazy psychopath whose HatePlague powers and ceaseless thirst for blood that ended up killing 75% of sentient life. The horror kicks in when you realize that Omega was exactly what Dr. Wily ''intended Zero to be.'' In fact, given what happens in the whole timeline, actually ''letting Dr. Wily win'' seems to be genuinely preferable to just thwarting his plans. As bad as his schemes got, they never went as far as what Sigma or later villains wanted.
** Remember, Wily became evil because his pride was hurt. Meaning if he won, it would be more or less just to prove he's better than Dr. Light. If he won, mankind would probably just have to deal with his ego for a couple decades until Dr. Wily dies (he's already quite old). Compare that with the nigh-undying [[WellIntentionedExtremist Sig]][[KillAllHumans ma]] and [[ItsAllAboutMe Doc]][[FantasticRacism tor]] [[DystopiaJustifiesTheMeans Weil]], and [[RootingForTheEmpire you'll be rooting for Dr. Wily in no time.]]
** Omega is exactly what Zero originally was before he [[HeelFaceTurn joined X's team]] and the Maverick Virus jumped to Sigma.
* Think of the attitudes humanity has towards genuinely non-violent robots: in [=MM9=], we see [[spoiler:the Robot Masters are still online when Wily finds them]]. In [=MMX6=], Gate's Reploids are killed off due to their potential risks instead of merely reassigned; in the context of this series, robots are basically sentient, so humans are willing to leave living people ''to basically starve to death, or outright kill them, out of convenience.'' Yet, people like Dr. Wily and Weil get to live, with no "kill on sight" orders established before being captured. How ''horrifically'' skewed are humanity's priorities towards robots and humans to even allow this to happen? The worst part about this? This means that Dr. Weil's BreakingSpeech ''[[StrawmanHasAPoint has ground.]]'' [[HumansAreBastards Only humans understand the joy of power, indeed.]]
** This goes double when you read [[AllThereInTheManual Mega Man Zero Official Complete Works]]; his reason for starting the Elf Wars was that he thought Reploids were getting off too easy for the massive destruction caused in the Maverick Wars, especially once the plan to solve the Maverick problem was to basically install anti-virus software and call things even. On the surface, it makes sense; each ''X'' series game chronologically takes place a few months after the last one, meaning not even half a decade had passed since Reploids were made before Sigma caused multiple wars and a ColonyDrop. And similar to how Weil fails to grasps his exile was his own fault, the wars were humanity's fault for making Reploids so powerful in the first place.
** All of them makes Weil [[UpToEleven even more terrifying.]] How? Because it means he had a good reason behind his FantasticRacism. ''[[WellIntentionedExtremist He]] [[JumpingOffTheSlipperySlope had]]'' '''JUSTIFICATION.'''
* Weil's "warning shot" with the Ragnarok was the only reason Zero & co. were able to defeat him. If Weil had just kept his mouth shut and improved his aim (which he had plenty of time for, since he was presumed dead from the destruction of Neo Arcadia), he could have used that shot to annihilate Area Zero ''or'' the Resistance base where Zero and Ciel were at the time. That's right, if it weren't for the VillainBall, [[TheBadGuyWins Weil would have won,]] [[YouAreTooLate right then,]] [[TheEndOfTheWorldAsWeKnowIt right there,]] [[DownerEnding with nothing you could do about it.]]
* From the manual: Weil was among the scientists who tried to resolve the Maverick Wars; specifically, he and his colleagues studied Zero's empty body. However, while Ciel's ancestor studied Zero's cognitive program for a cure, Dr. Weil viewed Zero's body as the ideal weapon to end the wars and used it to develop Omega, while Ciel's ancestor created the Mother Elf, which would be used by the original X to purge the Sigma Virus for good. Dr. Weil then proposed Project Elpizo, a plan to combine the Mother Elf with Omega to exert control over all Reploids. This put Dr. Weil at odds with X's ideals of coexistence between humans and Reploids. Undeterred, Dr. Weil placed a "curse" on the Mother Elf that turned her into the Dark Elf, and created clones named Baby Elves to control Reploids and make them fight each other in a massive battle royale. The panic and destruction caused the people to favor Project Elpizo, but X and Zero (whose program was put in a new body) recaptured the Dark Elf, forcing Dr. Weil to unleash Omega in the battlefield. Omega would move on to slay a large number of humans and Reploids before being finally defeated by X and Zero. Omega was sent away to Earth's orbit in the Forbidden Ark, while a group of humans converted Dr. Weil into a cyborg and cursed him to wander the wastelands of Earth as punishment for his crimes.\\\
Now remember when he said "I am The Devil"? Now consider these: Being one of the good guys at the start? Check. Being envious to one of the good guys that solved all the problems? Check. Cursing the tool (i.e the Mother Elf) that was previously used for peace, and created an AntiChrist to wreak chaos, just to spite said good guy? Check. Being banished to "hell" after all he had done? Check. [[MemeticMutation Falls from the "heaven"]] [[Franchise/StreetFighter like]] [[LargeHam lightning]]? Double check. Said good guy sacrificed himself to stop the whole mess? Check. Now sum them up, and then you'll think of him as ''[[{{Satan}} Lucifer, aka the Devil itself]].''
* Because of the destruction of Neo Arcadia, where else would the Resistance take the survivors but to Area Zero? (The presence of Colbor, the leader of the rescue team, in the Caravan's campsite during the ending supports this logic.) If so, then Weil's ColonyDrop wouldn't just destroy the environment and those dissidents in the Caravan, but probably also result in an instant KillEmAll. So much for a slow and painful death as Weil wanted the Neo Arcadians to go through.