In Zero's opening nightmare, he sees his own hands coated in the "blood" of dozens of Reploids. This isn't only a flashback to his dark past, but a prophecy of the blood that will soon be on his hands after slaughtering his friends in the Repliforce war.
X seems reluctant and Zero seems upset to declare Repliforce as Mavericks, so it was more likely someone off-screen who pushed this agenda. Who better than a first-hand Hunter witness such as Magma Dragoon? It's likely that he helped attest to Repliforce's guilt in the Sky Lagoon incident, under the orders of Sigma.
Zero's weakness technique against Cyber Peacock isn't Kuuenzan, but the fire-based Ryuenjin. Cyber Peacock is a virus/hacker, and one can beat viruses/hacking with a firewall.
Fighting Magma Dragoon with the Ride Armor is the ultimate disrespect. This guy killed thousands for a chance to fight X/Zero to the death and see their power himself. Bringing an unfair advantage into the fight is such a gutsy move, keeping Dragoon from getting what he wants while punishing him for his callous slaughter.
Unless Dragoon is up for the challenge.
Colonel's moves mirror the ones Zero uses in X2 and X5note Colonel's 3 Sword Beams = Zero's 2 busters + Sword Beam, Colonel's warp and slash is similar to Zero Nightmare's attack in X6, Colonel's Sword Plant move (which spreads out lightning on the ground) is Zero's Ground Pound move and Colonel's big ground wave move (under 50% health) is Zero's Genmurei, which does many things: it enforces his role as The Rival to Zero, shows that the Repliforce designers were taking inspiration from Zero, and shows what Zero might become if he became too focused on fighting.
By extension, this means that Iris was based on X because of their compassionate nature. This would also mean that the project that created Iris and Colonel was trying to make a fighter that combined X and Zero's best attributes.
The fate of Iris almost stops making sense given that Zero had his own Hunter unit back then and could've just assigned guards to protect her. Until you remember what Bass and King were like, and you realize that Zero also inherited his father's ego, albeit much more subtly than his siblings. This might have been foreshadowed in the intro stage: after their argument, Zero and Colonel beam out of the city, leaving an injured Iris behind.
The reason Repliforce's "Ultimate Reploid" failed is because they wanted her to have the same personality as X. If you want to know what happens when you make an exact copy of X without Light's meticulous 30 years of fine-tuning, take a look at Copy X in the Mega Man Zero series.
Ironically, some X/Zero shippers have Die for Our Ship tendencies towards Iris. Considering how Iris -another- was based so heavily on X, Zero falling in love with Iris actually supports X/Zero more than it hinders it.
Word of God is that Zero's berserk behavior as a Maverick in the flashback was the result of programming errors, which is to justify his being one of the more level-headed and collected characters in the Mega Man mythos. The logic is that the earliest prototype for both X and Zero is Protoman. Dr. Light analyzed Protoman's program and learned how to replicate his free will using stable code. Dr. Wily, however, focused on obedience over program integrity, and so did little to correct those errors.
Dr. Light's work also allowed him to build and program diagnostic computers that could repair errors in a robot's programming without compromising their core personalities and free will. Those computers would be the forerunners of the Reploid diagnostic machines Zero got plugged into for study and repairs after his first fight with Sigma.
Sigma's first form can only be harmed by fire weapons, which X and Zero obtain from Magma Dragoon. Guess like Magma Dragoon's subtly atoning for his actions from beyond the grave by giving X and Zero the means to hurt Sigma. Similarly, Sigma might have chosen to tempt Dragoon via appealing to his nature so that one of the Maverick Hunters holding his weakness to fire would no longer be a part of the Maverick Hunters anymore.
From a logical perspective, it also makes sense. Sigma is wearing a tattered cloak, which is certain to catch fire.
The Final Weapon suddenly makes more sense when you remember that Sigma previously operated out of large bases visible on the surface. Using just the previous games as a guide, Sigma nearly unleashed nigh unstoppable Battle Bodies, and nearly possessed X, the only one who ever defeated him. In fact, once you factor in Mega Man Xtreme 2 it makes even more sense: Sigma was thought destroyed at the end of Mega Man X3 and he still came back. Why risk sending two guys to fight their way through for a few hours when a Kill Sat does the job in an instant? Not even Sigma's viral form would survive getting blown to atoms.
Taking the Xtreme games into account, it's very probable an unspoken Time Skip occurred between this game and X3. Zero and Iris are in a relationship after being co-workers, Dr. Cain has clearly stationed himself elsewhere (or passed away off-screen by this point), and it's implied the Repliforce have been around for a while between games. Meanwhile, Sigma was thought dead, no one seems to even remotely cotton onto his being in charge of everything until he reveals himself at the very end, and Sigma himself outright appears in a reaper form like he came back from the dead — and then his final form looks ragged, hodgepodge and slapped together like he infected some pre-existing Repliforce tech in a last-ditch effort. He was already suffering Villain Decay the sequels would build upon, and it's after Dr. Doppler's anti-virus being used on him that Sigma simultaneously hit the Moral Event Horizon by losing a great deal of his sanity and morality.
In a more meta context, why does Dragoon get a lot of billing compared to many other animal Maverick bosses? He's a dragon and the first maverick to be based on a mythological creature. Since the series doesn't reuse animal/plant species in the games, the developers would have to make a maverick based on a dragon much more impactful.
Sigma's second form has gotten criticism for being a Marathon Boss, due to his repeatedly switching bodies and only being vulnerable for brief periods, all while he barrages you with tons of attacks. With the Final Weapon preparing to fire, this makes sense, as Sigma's doing everything he can to stall X/Zero from stopping it. Wearing them down and delaying them increases the chances of the Final Weapon going off without interruption, and even in the event it's stopped, X/Zero may either die or be too wounded to get off before it collapses. The only reason he failed was because General was still functioning and was able to give X/Zero an opening to escape, and even then that's because everyone assumed he died after X/Zero fought him.
If you think about it, Iris goes through the first four stages of grief throughout the game. For most of the game, she's in denial, given the pleas she makes to Zero and Colonel to stop fighting. After Colonel dies, she gets in the anger and bargaining stages, fusing with Colonel's programming in a failed attempt to be with him as Iris -another- and lashing out at Zero while at it. And after being defeated, she ends up in the depression stage, given what her final words are. Sadly, she dies before she could get to the acceptance stage, though if Project × Zone is to be believed, she reached that stage posthumously.
Colonel appears in both X and Zero's versions of events, but Iris only appears in Zero's. This could mean Iris died in the Sky Lagoon incident in X's version of the story, further fueling Colonel's headstrong actions.
The canon version of X4 appears to be a combination of X and Zero's stories, if what characters say in X5 is accurate. It seems Zero dealt with Iris and Colonel more, while X dealt with Double and General more. As a self-contained narrative, however, it totally looks like Iris may have perished in X's story.
In Storm Owl's stage, some of the ships overhead are firing lasers to slow X and Zero down. The stage takes place over a city, and your character never stops those ships- it's implied stopping Storm Owl would make them surrender. How many people are getting killed by those lasers and, if the player takes their time, how much death are X and Zero indirectly responsible for?
The Repliforce think that they're doing the right thing by refusing to put down their arms and fighting for a utopia for Reploidkind, even if they supposedly don't wish to harm humanity at all in the process. Now think about the story from their perspective; more specifically, Colonel's perspective. How would anyone take being told that they, a person who's dedicated their lives to fighting against the Mavericks is under suspicion of being a maverick themselves? Worse, one who laid waste to a city they'd spent the entire time protecting? Now imagine this is coming from someone he considered a friend. Is it any wonder Colonel snapped? Is it any wonder General made the choice he did when Colonel all but confirms his fears about the humans and their potentially unfair treatment of Reploids? It gets even worse when you consider Colonel and Iris's creation was basically a rush job, with the higher-ups sending them into war not long after their births; and the fact that Colonel was supposed to have a degree of pacifism, but the tests of it failed (due to it clashing with his fighting spirit), forcing the scientists to put them (i.e the A.I programming that chooses peace) into Iris. He basically has no way of making peaceful resolutions.
Not to mention that X5 confirms there were survivors of Repliforce. Never mind the whole honor issue, imagine if they learned how the Maverick Hunters and the government were becoming more paranoid and violent against Reploids, as bosses in later games confirm, and realized that they were the ones who set them on that path.
Here's another one for Repliforce: considering how heavily armed they were, and their infamous morality, you quickly realize that Sigma probably didn't need to do anything; Repliforce was a powder keg. The manual also points out that they're "potentially dangerous".
Especially since at least two Repliforce commanders were attacking civilian targets, specifically Storm Owl and Jet Stingray. The city Jet Stingray attacked was even described as being "decimated". So much for not wanting to harm humanity.
Actually, Iris was the one supposed to be created, as seen in X Dive. A recent update gave us Iris -another-, who is the Ultimate Warrior Repliforce planned on creating. Although, technically, Iris -another- is pretty much the Colonel of Repliforce herself, due to Colonel being half of her.
Colonel was built with the aggressive half of the project, the honorable warrior that lives for battle. And they put him second-in-command of a military police that were meant to invoke martial law but not overstep the Maverick Hunters. It's no wonder he refused to surrender along with the rest of the Repliforce; he's literally built to fight and someone was stupid enough to put that in co-leadership of an entire armed faction. Sigma didn't just have a powder keg of tensions, the whole force was practically rigged to blow by fools making war weapons.
If you want horror and a little bit of weirdness, realize that Iris and Colonel were failed attempts to recreate X — and Iris has X's green eyes while her compassion design was meant to mimic his own. Zero not only fell in love with a Reploid that was a partial attempt to recreate the nice parts of his best friend and comrade, but subsequently murdered her without much choice in the matter. Is it any wonder that he seems to get both more standoffish and even more self-sacrificing in protecting X going forwards?
When Iris is defeated and put on death's door, notably she as a whole goes down, rather than solely Colonel's core. When she espouses her last words about how she wishes she could create a place for her and Zero with only Reploids, this sounds like Fantastic Racism, but the reality is probably closer to her love for Zero barely overcoming the mix of Colonel's own ideology and programming merging with her own; she's effectively Zero's lover and best friend at the same time suffering a case of My Skull Runneth Over and barely managing to die as herself at the end.
At the end of his story, X is worried that he'll go Maverick someday, since Repliforce turned on their own accord. Repliforce turned to protect themselves and make their own home, not to attack humanity, establishing that "Maverick" can be more broadly applied than in the last games. Jump forward to the gap before the next series where X, after having established a practical utopia as its ruler, sealed the Dark Elf and abandoned his post without appointing a successor, and in the series proper where he could've made things easier if he appeared before his minions and talked to them, but didn't so he could "rest". He indirectly put everyone in danger of getting killed at some point. He really did go Maverick after all.
This doubles as Fridge Brilliance when you remember that X's final death in the Zero series happens as a result of expending the rest of his energy as a cyber elf to stop Omega (the original body of Zero) from mind controlling all the Reploids in the resistance base, making Omega indirectly responsible for X's demise. When you take the above entry into account, this means the Foreshadowing from X4 does ultimately come to pass: X inadvertently puts everyone in danger by abandoning his post- an action that can be considered Maverick, then later the original body of Zero becomes the cause of his final demise. Though keep in mind that the reason X needed to "rest" in the first place is because he had lost his compassion due to all the years of endless fighting wearing it away, and the original plan was for him to actually lose his mind from this and become the psychotic Knight Templar we eventually got with Copy X. For all of his efforts, a happy ending was never in the cards for X. His only options were to either go crazy and have to be put down by his best friend, or cause the creation of the genocidal Copy X by abandoning his post, both of which involve him putting everyone in danger and dying by Zero (indirectly or otherwise).
Except for one thing: until the events of the third game, where he pretty much sacrificed himself, it is unknown how much help he could have been. It's really unknown whether he could have majorly interacted with the real world before his body got destroyed, and whereas Zero took the help he gave because why not, it's unclear whether the guardians would have even recognized him, especially with Copy-X being there and especially when we don't know if his help was even needed before Copy-X and his arrogant shenanigans (probably not, since the guardians seemed to be faring well).
The entire Iris and Colonel problem of one having the compassion and the other having the combat focus is just one of many highlights of how dangerous Reploids are in this series. Even if we discount what Sigma and his forces build, a great deal of the Mavericks our heroes destroy are some variant of combat machine, bodyguard, researcher — and all of them have inherent battle capabilities, to the point that they're easily stronger and more powerful than just about all of the mechaniloids and old robots in their stages. Which means humanity keeps building insanely powerful machines alongside their operator, support and even citizen models, giving them full sentience as thinking Reploids, and then trying to force them into a subservience after the fact or simply sending them off to go do battle and police the world. Is it any wonder Earth effectively became a giant wasteland in the aftermath of people constantly designing war machines and basically delivering Sigma a never-ending supply of destruction he could manipulate or infect? And besides Dr. Cain and the one guy in the intro of Maverick Hunter X, we never see any humans in this series nor anyone to hold accountability for entire extinction events — something that carries onto the Mega Man Zero series with a certain new antagonist...
It also raises the question of why so many Reploids are being designed for warfare and conflict. As far as the X series bothers to say, it's entirely because of the Maverick Wars, but Sigma and the Maverick Hunters existed even before the Zero Virus was unleashed, and that means someone as powerful as Sigma was either designed or refactored to kill his own kind if they went haywire. No one ever seems to learn their lesson, dial things back or realize they're making it worse, instead pushing the world into a Lensman Arms Race to fail to solve a problem with stronger and stronger creations, a problem humanity created by accident just because they made Reploids.
And if Dr. Weil's later discrimination involving the Three Laws-Compliant nature of old robots that he throws at Zero is anything to go by, there's a strong possibility that whether due to the Maverick Wars destroying most of the world, or due to just plain ignorance even up to the higher echelons of the surviving humanity, there's likely an uncomfortable number of humans who are either taught to or intentionally believing that Reploids were created to serve mankind and little more. Given the amount of hell that Reploids go through, right up to mortality imposed by law by the time of Mega Man ZXunder the false pretenses of equality by manipulators intending to reset the world in their image, there's grounds in the theory.
Speaking of Colonel and Iris' creation, as the manuals stated, the two was originally planned to be a single Reploid with a kind of programming close to X, i.e a powerful, honorable fighter who's at the same time compassionate and values peace. But then the result comes out as flawed and potentially dangerous to itself (the programming cannot reconcile between the two extremes), so the Reploid was then split into two, each inheriting different aspects of X. Iris later does try combining Colonel's "core" with hers, but it pretty much overclocks her body. The horrors come in the potential that X's own programming might one day eventually fail, which would be dangerous to him... or other people. This is at least shown in X7 and Command Mission, the former where X falls too far on the "pacifist" side while the latter is his most "destructive" incarnation. The original plan for Mega Man Zero was that X would discard his pacifism and concerns for his enemies after countless wars, becoming a ruthless Knight Templar that Zero has to stop; this didn't come to pass, but what did come was that X almost fell over said edge, only stopping himself once he realized it. A few of cyber elf X's comments in the games also hint at his ruthless tendencies that he tried to suppress.
The flashback sequence:
When a red maverick wiped out a unit of Maverick Hunters, Sigma was sent in to stop him. Now remember that all the Reploids, including the hunters and Sigma, were created thanks to Dr. Cain discovering and studying of X several years before Zero woke up and caused trouble. Had someone discovered Zero's capsule and awakened him before Dr. Cain found X, the Ax-Crazy Zero could've slaughtered every human and robot alike. And considering very few reploids can stand up to Zero, human and Mega Man (Classic) style robots would have been largely powerless to stop him.
The berserk Zero could've done some damage, but as Mega Man Zero 2 shows, he could only last for so long. Especially since he doesn't seem to have access to the enhancements we see in X1, and possibly can't access them due to his unstable mental state. That said, while Zero's mental flaw left him violent and insubordinate, our only hints to what he was really like are the non-canon Awakened Zero and Omega, who was programmed by someone far worse than Dr. Wily. He might've been like Bass, and still had some morality.
Taking the flashback with Zero's dream sequence, and it's implied that the Hunter unit released Zero instead of calling for back-up. We think Zero killed them outright, but as noted above, we don't know what Maverick Zero was like, and we don't know how those Hunters reacted to Zero. He could've acted in self-defense, and was contemplating his actions when Sigma walked in. And when the fight began, Sigma played around instead of going for the kill. That fight could've exacerbated Zero's flaw, as that was the only time he was gleefully violent. Sigma would've defeated Zero had he done his job properly. That Hunter unit would be alive had done their job right. The Maverick Hunters were already becoming arrogant, with what they became in Mega Man Zero being the inevitable result of the Hunters being controlled largely by Reploids and not a joint operation between Reploids and humanity. Of course they'd be "far too eager to please the humans" when humans still treat them tools.
There are some darker implications stemming from Iris staying with Zero after the intro stage:
Since she was recovered by the Maverick Hunters, Repliforce might have written her off as either a POW or as a traitor for accepting their aid.
Even if she was welcomed back, her pleas to stop the war would probably end with her being punished since she'd be arguing with Colonel, who is her superior officer, and General, their supreme commander.
Speaking of which, imagine what Colonel must've been thinking this whole time. Seeing her at Memorial Hall must've been an immense relief, even though it would be the last time he'd ever see her.
Zero tells Colonel that he made sure Iris was safe in the Opening Stage, before their argument. So he knew Zero saved her, he just needed a reminder at Memorial Hall.
