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.
Weil is also a mass murderer despot. The spirit 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 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 Three Laws-Compliant 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 Mega Man 7? 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 old self. Remember that in X2, Sigma made reference to Dr. Wily for Zero being his last creation. 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 Ax-Crazy within 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 Japan-exlcusive e-Reader cards also appearing in the Compilation Re-release on the DS (this time in all regions) includes a poster of 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 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 Project X Zone, Iris is brought back thanks to the representatives of .hack. 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 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 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. Word of God 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.
In previous Mega Man series, the first stage of the final boss has a unique boss theme not used anywhere else in the game. Not so with Copy X; his first-stage boss theme in Mega Man Zero 1 is the same "Crush" that was used for every other boss encounter. Copy X isn't X. He's not on the same level as Sigma or Dr. Wily before him. As far as Zero is concerned, Copy X is just another boss.
The battle music for Copy X's One-Winged Angel form, "Fake", is also a rearrangement of the battle music used for Vile and Sigma's fortress bosses in the original Mega Man X. To date, Vile has never been the Big Bad in any game he's appeared in; the most he's ever been is a pawn or The Dragon for Sigma, the X series' perennial Big Bad. Next time we see Copy X, he's a pawn for the Zero series Big Bad, Dr. Weil, who's also been pulling the strings for the entire series. Copy X is a fake Big Bad.
It was also in the underground lab Ciel found Zero in, so that data probably included backups of Zero's memories, in addition to blueprints for his weapons. So this mission might also be why he never completely recovers from his Identity Amnesia.
The low-orbit spaceship that Omega was exiled to is shaped like a sword. Omega was an almost literal Sword of Damocles hanging over the head of Neo Arcadia.
The appearance of Colonel alongside Vile, Agile, and Bit initially seems odd... until you realize how draconian Neo Arcadia has become; if theyd label someone like Alouette as a Maverick, they would of course lump Colonel in with those sorts of crooks!
Also, Zero didn't canonically meet or battle Agile and Bit. But Phoenix Magnion isn't pulling those images from Zero's past. He's pulling from X's. Vile, Agile, Bit, and Colonel are all fortress bosses in the first four games of the Mega Man X series, respectively.
Toss in Zero himself as the fortress boss from X5, and you have the entire canonical Mega Man X saga represented in this one attack.
The battle with Omega at the end of the third game can be a bit of an Anti-Climax Boss, given that for his massive pool of moves that can potentially be quite dangerous, a properly-upgraded and prepared player can potentially take him down in less than a minute. But this makes sense for two reasons: one, both Zero and Omega are wielding Z-Sabers, which have rendered short work of just about everything else, so this turns their climactic duel into Rocket-Tag Gameplay. And two, besides all the EX-Skills and chips he can acquire, including one that lets him phase through attacks, Zero's memories and experiences grant him a significant advantage in precision and effectiveness over Omega basically jumping around and blowing everything up recklessly - after all, Zero in the copy body beat Omega once before alongside X, and that was when he was fresh to that body.
Players new to the Zero series may wonder why charged shots and sabre slashes do so much damage to bosses (chopping off a good quarter of their life bar), in comparison to the X series, which may see, at most, three or four ticks off of the health bar at best. A clue might be found in the design overhaul the game took - by getting rid of the bulkier designs (such as the heavy armor and huge metallic boots), the Reploids have effectively traded defense for a slimmer, more streamlined design.
Omega, the Ax-Crazy psychopath whose Hate Plague 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 Sigma and DoctorWeil, and you'll be rooting for Dr. Wily in no time.
Omega is exactly what Zero originally was before he 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 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 Breaking Speechhas ground.Only humans understand the joy of power, indeed.
This goes double when you read 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 Colony Drop. And similar to how Weil fails to grasp that his exile was his own fault, the wars were humanity's fault for making Reploids so powerful in the first place.
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 Villain Ball, Weil would have won,right then,right there,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. Falls from the "heaven"likelightning? 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 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 Colony Drop wouldn't just destroy the environment and those dissidents in the Caravan, but probably also result in an instant Kill 'Em All. So much for a slow and painful death as Weil wanted the Neo Arcadians to go through.
The fact that the rank-and-file Pantheon troops look like Cyber Cyclops versions of X. Zero spends four games butchering robotic mockeries of his best friend en masse.
The Retirement Facility is already creepy enough with dead Reploids everywhere, but once Weil takes over, theres probably also bloody dead human remains in there too.