A bit of unintentional Fridge Brilliance came with the renaming of the Mavericks to Guns N' Roses references. The person who did it just did it because her husband was a fan of the band, but given all the other music-themed names in the Mega Man franchise, it also fits in that category.
Why is the Enigma cannon called that? There are a few reasons:
First, the entire franchise comes from Japan, and we all know how Japan is so much in love with cool-sounding foreign words. Second, its mere existence in X5 is also the reason why it was called Enigma. There was never any mention about said weapon from previous games. The closest we could have for a gigantic laser cannon is Final Weapon, and we all know what happened to it. When X5 came, it just came out of the blue mysteriously. Finally, the most important reason why the Enigma Cannon was named like that was because...well, it was an enigma. At first, people kept on looking for the meaning, from any available and possible standpoint, before they just give up. There might be a real meaning of its name, other than just for sounding cool. But until someone finds that meaning, it will stay as a mystery, hence the name Enigma. The name pretty much self-demonstratesitself.
In X4, what appears to be the Enigma Cannon can be seen in the background of Web Spider's stage, and it later dominates the backdrop of Web's chambers. He must have been a Repliforce officer associated with it! Not to mention the real reason why Repliforce was building Enigma: it's an anti-aircraft cannon meant to both defend the Final Weapon from incoming threats and take it out if it's compromised. After all, what better weapon to use on a giant space laser pointing down than a giant space laser pointing up?
Zero's virus power boosts may be linked to his rocky emotional state. If the Maverick Virus, and by extension the Zero Virus, are based on the Evil Energy of Mega Man 8 (as it is widely theorized), then Zero's darker emotions are what feed the virus, which in turn powers him up. Consider that Zero was originally an uncontrollable berserker, but there's no reason Dr. Wily didn't want a berserker. As Zero says in his own series, he only fights for those he believes in: he has no higher ideals like X. Plus this plot-point came after X4, where Zero would undoubtedly have some self-loathing after Iris.
X's reason to fight non-Awakened Zero may seem contrived: he's just worried that Zero is getting stronger because of the Zero Virus? Well, X's reasoning was likely more of a justification for what he knew had to happen. X knew since X2 that Zero had a dark origin and that they would inevitably fight to determine the world's fate, a premonition which only grew clearer in each subsequent game. X realizes this is that prophesied moment, and they are fated to fight. He simply cannot avoid it any longer.
As for Zero, he is heartbroken to be confronted by X like this. What X communicates to Zero is "the Hunters don't trust you — I don't trust you — to not destroy your friends with your power." Still struggling with the blood of Iris and Colonel on his hands, Zero cannot stand being mistrusted and treated like a danger or a liability any longer. He's been fighting his destiny of destruction for so long, and now that even his closest friends won't back him up anymore, it pushes him to his breaking point.
Sigma's sleek, simplistic first form resembles the simple designs of X and Zero, more so than any of his previous bodies. When you take into account that you fight him in a room with X and Zero's capsules and blueprints prominently displayed in the background, it becomes clear that Sigma is intentionally mimicking X and Zero's appearances.
Dr. Light's seemingly miraculous feat of walking out of his capsule to repair X may seem weird, but it makes sense once you realize that the event takes place in Zero Space (the final stages) where Cyberspace and the real world merged due to the intense amount of viruses at the site. It thus would allow Light to materialize himself from his capsule (presumably the one in Zero Space #3) to catch up to X.
This also makes sense why X5 was meant to be the last in the series. If you kill Sigma in real world, he can just escape to cyberspace and hijack a new body. His source of regeneration is in cyberspace, and if you kill him in cyberspace, you kill him for real.
The "bad path"
You may be wondering why this is considered X's "bad" ending. After all, despite Zero's death, X is fully repaired and the world's recovering, with X chasing his dreams of a utopia. While X's talk of utopia can seen as Foreshadowing for the formation of Neo Arcadia, with how much Zero being alive factored into the backstory of the Mega Man Zero series, it's unlikely those exact events will occur. What is more likely to occur is that X will have no friends: Zero is dead, and Sigma stayed dead as well, so Axl won't be created. And, as the backstory of the Mega Man Zero series suggests, X never gained any new friends in the 100 year gap between his series and Zero's. Unless Alia's feelings for X in X6 are reciprocated, who's to say that X wouldn't eventually break from the strain and have the Face–Heel Turn that Keiji Inafune had originally planned for him? note And to make things worse, this would be X at the peak of his power, as sealing the Mother Elf with his body split X into his Cyber Elf form and the Four Guardians.
Considering that X doesn't remember Zero and doesn't have the Z-Saber, X6 would be impossible under this timeline. Zero's body wasn't recovered, so Gate was unable to recover any samples of Zero's DNA, and in turn was unable to recover Sigma. It also means that despite the game's implications that he was alive as an AI, Dr. Wily wasn't able to recover them either. Since Awakened Zero's personality is a mystery, being non-canonical and all, Wily might've been Killed Offscreen by his own creation.
You would think that all the boss Reploids would have the Sigma logo under their health bar like Dark Necrobat (who was already a Maverick before the Eurasia Incident). Instead, they have a simple skull. Why would they go to the trouble of only giving Necrobat a special logo? Because Necrobat is the only boss you fight that's full Maverick; the others were only infected mere hours ago and are still mostly themselves. They fight X/Zero either out of some grudge they wanted to settle anyway, or because they want to be put down before Sigma takes hold.
This, however, brings the question: why do X and Zero have the skull emblem in their duel, rather than their own emblems? Or, even better, the emblems of their respective creator? Especially blatant when you consider that Wily's emblem is in the background in the fight. Well, Zero does get a pass: all of Wily's bases have a skull motif, so it's a more subtle nod to Zero being a Wily robot. X, however, doesn't get such a pass.
In Zero's ending, he admits he was built to be a killer and must stay dead to preserve peace. However, he is soon resurrected in X6, meaning he can't even enjoy the sweet release of death. No wonder he was so quick to go into a coma for research after that game!
He doesn't get sealed until after the X series as a whole, but he's notably much more bitter in X7, so at least to some degree his Knight in Sour Armor status only got amplified.
When X and Zero have their fight, Sigma appears to destroy an unconscious X. Canonically, Zero fends Sigma off. But in the Maverick Zero route, he dies Taking the Bullet for X, as being defeated in his Awakened form took a bigger toll than what canonically happened. And since Dr. Light erases X's memories of Zero, to the point X's mind can't accept information related to Zero, not only will Zero be remembered as just another casualty, but X will never know his friend's last act was to save his life. The only silver lining is that Zero's fall from grace will be hidden by Signas and the brass at Hunter HQ.
is considered X's "bad" ending. After all, despite Zero's death, X is fully repaired and the world's recovering, with X chasing his dreams of a utopia. While X's talk of utopia can seen as Foreshadowing for the formation of Neo Arcadia, with how much Zero being alive factored into the backstory of the Mega Man Zero series, it's unlikely those exact events will occur. What is more likely to occur is that X will have no friends: Zero is dead, and Sigma stayed dead as well, so Axl won't be created. And, as the backstory of the Mega Man Zero series suggests, X never gained any new friends in the 100 year gap between his series and Zero's. Unless Alia's feelings for X in X6 are reciprocated, who's to say that X wouldn't eventually break from the strain and have the Face–Heel Turn that Keiji Inafune had originally planned for him? note 