That's an immovable law of nature, and has been so since at least the seventies. Trying to pretend for any amount of time that this isn't one of the bedrock foundations of the Marvel Universe is pure, disorienting folly. It doesn't even matter that, in real-world terms, most people would concede the rightness of Iron Man's position: if (and of course, this is the kind of "if" through which you can drive a Mack truck) super-heroes were real, of course we would want them to be trained and registered. But because this is comics, we also knew that Tony was wrong for siding against Cap. Sure enough, the fact that he proceeded to build a Negative Zone prison, put murderers on the payroll, and build a homicidal clone of his dead best friend proved in short order that Cap had been right from the beginning. It didn't help that once the Civil War was over Tony's national security infrastructure was co-opted by the Green Goblin, an event that only reinforced the fact that, even (temporarily) dead, Cap was still always right.
So, on to AvX. Again, we're presented a seemingly even-handed conflict between Captain America and another marquee hero, and expected to believe that it's a fair ideological fight. The only difference in this respect between Civil War and AvX is that while you could at least make the argument that, in a quote-unquote "real world" context Iron Man probably had a point (even if, in-story, we always still knew Cap was right all along), there really doesn't seem to me to be any reason whatsoever for pretending that Cyclops had any rational justification for his actions over the course of AvX #1-12. There's no real suspense here. In both practical and ideological terms, Cyclops wasn't just wrong, he was spectacularly wrong.
In this context, it might be more convenient to split AvX into two distinct ethical questions: for the sake of argument we'll call them the Phoenix Question and the Mutant Question. The first is a situational question, the second is conceptual. The former is easier to answer, while the latter points not merely to the weaknesses of Cyclops' argument but the larger problem of how Marvel has spent years deliberately undercutting the premise of the X-Men.
First, the Phoenix. The very first part of AvX was a prologue printed in the first Marvel Point One book, from the end of 2011. In that story the new Nova, Sam Alexander, witnesses the Phoenix destroying / consuming an entire planet - Terrax's planet, incidentally - while making a beeline for Earth. The new Nova reaches Earth at the beginning of AvX proper, carrying the warning that the Phoenix is loose, heading in the direction of Earth, and destroying planets left and right. Given that, it is more than reasonable to expect that the Phoenix coming to Earth does not bode well for the planet and its inhabitants.
Now, step back from the book a moment and think about the difference between the two levels of knowledge to which we, as readers, are privy. Certainly, we as readers know that we're reading fictional stories set in a super-hero universe, and that if the Phoenix is heading in the direction of the Earth it has business on Earth, otherwise there would be no purpose in telling this story. But we can't loose sight of the fact that, in-story, the people in the Marvel Universe living under the cloud of this impending threat don't and can't know precisely what the Phoenix is doing. Remember, the Phoenix is not merely an unimaginably powerful cosmic entity, but a singularly inarticulate cosmic entity. Galactus declaims, the Stranger exposits, but the Phoenix doesn't actually say anything: it takes hosts, and the hosts speak, but unfortunately when the hosts speak they have a tendency to say things like this:
. . . and then go on rampages where they destroy entire solar systems and planets full of peaceful broccoli people.
So even though we as readers know the Phoenix is probably coming to Earth to do something related to M-Day and Hope Summers and all that jazz, the people in the story don't know this with anything resembling certainty. And the problem is that this is a situation where being wrong doesn't just mean people get hurt, or a few people die - it means that everyone dies. With the Phoenix on the way to Earth, there was a not-zero chance that the Phoenix intended to destroy the Earth for whatever reason, or maybe even no reason at all. So whatever reason Cyclops had for thinking the Phoenix may have been headed to Earth for benevolent reasons are essentially moot. If there is a not-zero chance that the Earth might be destroyed, it isn't just irresponsible to stand in the way of a solution to the problem, it's downright villainous. Dr. Doom would gladly risk the destruction of the Earth for a chance at absolute power - Cyclops may believe his motivations were more noble, but the fact that he was willing to gamble a non-zero chance of an extinction level event against the health of the mutant race is unacceptable.
I've said many times before in multiple contexts that I've never been a fan of the Avengers being a fully sanctioned branch of international law enforcement. Marvel heroes, even the "establishment" heroes like the Avengers, always got by on being vaguely scruffy and disreputable, so being licensed and bonded agents of S.H.I.E.L.D. presents the concept at a disadvantage and, for what its worth, results in static storytelling. But if you're going to insist on this status quo for the Avengers (and, given the success of the movie, it's likely to be the status quo for a long time to come), then you need to show the Avengers in a position of unambiguously defending the Earth from external threats. That's precisely that the team does in AvX: whatever Cyclops' rationalizations are, the fact is that in the context of the story his actions materially contribute to a not-zero chance of the planet Earth being destroyed. The moment the X-Men decide to strike out against the Avengers and gamble the safety of the planet against the well-being of a small minority it becomes impossible to sympathize with them. And what's more, it's not even as if you can make the argument that the Avengers were really trying to persecute the X-Men, put the surviving mutants in camps or Negative Zone prisons or whatever else the government did during the Civil War: all they wanted to do was take Hope as far away from Earth as possible in an attempt to forestall the not-zero chance of planet-wide extinction.
(It's also worth mentioning that later on, at the story's conclusion when Hope actually does receive the Phoenix force, she is only able to control the force and use it benignly because she's spent months being trained in K'un-L'un by Iron Fist, Spider-Man, and Captain America. This wasn't something Cylcops or even Cable did for her.)
From the very beginning of the story Cyclops is wrong about the Phoenix because he simply ignores the possibility that the Phoenix is coming to Earth for anything other than to help jumpstart the mutant race, even though - in-story - he has no reason to really believe that aside from a handful of possible coincidences and hunches. Hope could have been groomed to serve as the Phoenix's new host not out of a desire on the part of the Phoenix to help humanity, but because of any number of other strange and unknowable reasons that only make sense to cosmic birds of fire and death. I know I keeping harping on this, but I simply can't move past the fact that regardless of why Cyclops believed the Phoenix's arrival would be positive development, the fact that there was a not-zero chance of him being proven wrong is simply unacceptable. The stakes, in this instance, were too high for the Avengers to do anything but what they did.
Moving on from the question of the Phoenix, we are left with the larger question of why exactly Cyclops is motivated to do what he does in order to preserve the mutant race in the first place. Already we see a serious problem, but we need to back up a bit to understand exactly why this was such a problem. When the Scarlet Witch said "no more mutants" at the end of House of M, it didn't immediately strike me as a terrible idea: cut down the number of mutants from the absurd number that had popped up since the mid-nineties (and especially during Grant Morrison's tenure), bring the books down to a status quo more or less resembling the way the line looked from 1963 up through the early nineties. Mutants had been rare but not so rare that they couldn't always find new mutants about whom to tell stories, and most importantly there weren't so many of them that the sheer weight of demographics put a strain on the suspension of disbelief in the wider Marvel Universe. That was pretty much the way the books worked up through to the point when Claremont left in 1991, so a return to that premise seemed to me like a good decision at the time.
But that's not what Marvel did. Instead of just cutting down the number of mutants and going forward from there, they picked a random number (198!) and stuck with it as their status quo from that point forward. There could be no more new mutants until Wanda's spell was undone. This wasn't a story Marvel had any intention of telling until 2012 - so, from 2005 to 2012, the X-books were stuck running in circles in the shadow of a larger meta-narrative that everyone reading the books knew they couldn't actually resolve. There was a giant scab at the center of the franchise that could not be picked until the powers-that-be at Marvel were ready to do so.
In the meantime, the books themselves made a subtle but disastrous decision. It might seem like a small point, it might even seem insignificant - but the X-Men themselves made a practice of referring to mutants as a "species" and a "race." Notice I even did so earlier in this essay. They even had a crossover event called "Endangered Species." Think about this for one second: the entire premise of the series from the very first issue of X-Men back in 1963 is that mutants are not a separate species. Professor X says that the X-Men have "extra" powers that give them the responsibility to protect "normal" humans against the predations of "evil" mutants who believe their powers give them the right to dominate humanity.
Magneto is the first character to utter the phrase "homo superior." Professor X asserts that mutants are a part of humanity, and that their "extra" powers do not give them extra rights to exert their superiority over those who are not so gifted (or cursed).
This is a basic definitional fact of biology: mutants are not separate species. Mutants only become separate through the process of speciation. Mutants precipitate speciation through the process of natural selection, but mutants themselves are not separate species. This is certainly true in the Marvel Universe, where it has long been established that mutants do not necessarily breed "true" (meaning, it's possible for mutant parents to have "normal" offspring), even thought many subsequent stories have muddied these waters for various reasons.
This, in any event, is the most basic premise of the X-Men: mutants are humans who have received "extra" powers through accident of birth and are sworn to protect humanity from those mutants who believe their powers set them above or against the human race. The books have often served as a metaphor for civil rights movements - from the end of segregation in the sixties through to the rise of feminism in the seventies and the fights against Apartheid and for gay rights in the eighties and nineties, the men and women behind the franchise did a good job of keeping the books tethered just enough to a real-world understanding of prejudice and the mechanisms of historical change. It was never a good idea to press too heavily on the subject, since the books are first and foremost fantasy - and therefore not at all contiguous with actual real-world civil rights struggles - but as fictional metaphors go the X-Men was a pretty handy vehicle for exploring surprisingly heavy themes in the guise of children's entertainment.
The problem is, as I said, because it's a fantasy metaphor it doesn't pay to put too much weight on the analogy. It works in broad strokes, but once you get into the thicket of the practical "realities" of mutants in the Marvel Universe, you run into problems. M-Day is ran into these problems head-on, with a vigorous enthusiasm that belied that fact that the people in charge at Marvel did not understand how they had profoundly crippled the franchise.
Mutants aren't a separate species, anymore than black people, jewish people, GLBT people, or disabled people are separate species. That's the whole premise. Their mutations are completely random. That is also why some mutations are benign and some are not: some people get really awesome Omega-level reality-altering telepathic powers, some people get turned into hideous monsters who have to live in the sewer. You don't get too choose your genetics, the series maintains, so prejudice against people on the basis of genetics is inherently wrong - and to go one step further (attempting to keep pace with advances in queer studies and disability studies, among other disciplines), you are entitled to live however you want to live and be recognized in whatever way you wish to be recognized by a world that has no right to impose its idea of biological determinism upon you.
All well and good. The problem is that if you look at it too hard, the rules regarding real-world minority concerns don't quite work for mutants in the Marvel Universe. And the reason it doesn't quite work for mutants is that mutation in the Marvel Universe doesn't just come in the form of benign godlike powers that still leaves the recipient in possession of fantastic good looks and a super-ripped bod. Who wouldn't want to be a mutant, if that were the case? There is a not insignificant portion of mutants in the Marvel Universe - and there has been ever since Stan & Jack created the Mortimer Toynbee in 1963 - whose mutations resemble something more along the lines of a physical disability. This is why my least favorite X-Men stories have always been those stories that deal with the idea of a "mutant cure" as if it were some kind of terrible existential threat to mutantkind. Even putting aside an early outlier like the Toad, since Chris Claremont created the Morlocks there has always been a sizable group of mutants who haven't been pretty and perfect like the X-Men (and, come on, even Nightcrawler is beautiful), who would probably have no qualms whatsoever about taking a "cure" that would enable them to live something resembling a normal life once again.
The entire premise of the X-Men is that mutants are people, too, they just happen to be different from "normal" people, and furthermore, the idea of normalcy is overrated and hegemonic. That's fine, and certainly one of the strengths of the X-Men's original premise. But there are plenty of mutants who would probably love the opportunity to live "normal" lives. And we're not talking about something hideous and disgusting like the "gay cure" groups who brainwash LGBT kids into thinking they need to conform to some idea of "normal," we're talking about someone like Rockslide who no longer has a human body or working sex organs (as covered in one of the last issues of Avengers Academy) or Glob Herman, or even someone like Strong Guy
whose powers force him to live in severe pain and be at constant risk of suffering a fatal heart attack.
In our "real world" mutants are as likely to have cystic fibrosis and muscular dystrophy as something benign like heterochromia. Traditionally, this was another one of the franchise's strengths - acceptance of differences, helping people learn to accept themselves and live with and celebrate whatever it was that made them "extra" ordinary, for better or for worse. But the moment Wanda said "no more mutants" and the X-Men became fixated on trying to "restore" the mutant race, this simple and supremely pliable premise was warped almost to the breaking point. Mutants aren't a race, they aren't a species. That's Magneto's logic, that's Apocalypse's logic, not Professor X's logic, and certainly not the logic behind forty-odd years of X-Men stories. Mutants are part of humanity. Mutants don't get to choose how they're born. Mutants should be able to live however the want without fear of prosecution. Mutants should use their powers to help those without, not because they're better than normal humans but because they are, fundamentally, the same. And being a mutant is as much a curse as a gift.
This premise went out the window the moment M-Day happened. The series' most basic metaphors were annihilated. It's not about toleration and acceptance anymore. Suddenly the X-Men started talking about "the mutant race" and "the mutant species." It became important to restore the X-gene to the world, so there would be more mutants - no one ever said exactly why this was so important, since it didn't actually contradict Professor X's original motivations for founding the X-Men. Making the conscious decision to restore the X-gene didn't just mean there would be more supremely powerful, beautiful mutant demigods walking around (who could object to that?), it meant that there would also be more Glob Hermans. Sure enough, the first three new mutants we met in Jason Aaron's Wolverine and the X-Men after the conclusion of AvX are a kids covered in eyeballs, a girl who can turn into a were-shark, and a half-lobster half-boy. Not superstar mutations by any stretch of the imagination - serious, life-altering conditions that most people would probably rather not experience.
I must have missed something. I must have missed the part of AvX - or really, any of the years of X-Men stories leading up to the crossover - where Cyclops took the time to explain exactly why the mutant gene simply had to be restored, why having a handful of new and beautiful godlike mutants was worth the price that there would almost certainly be just as many, if not more mutants who weren't so lucky, and received the superhero equivalent of cystic fibrosis and muscular dystrophy for their troubles. It's one thing if they had randomly been born that way, but a number of people fought long and hard to ensure that they would have the "freedom" to have their lives irrevocably changed for the worse. Those people were led by Cyclops, and at no point during the course of AvX does he ever actually explain why cursing Mudbug, Eye Boy, and Shark Girl to live terrible lives was a necessary sacrifice for the good of the "mutant race."
At the very end of AvX, after Cyclops has been stripped of the Phoenix power and placed into custody, he learns that new mutants have begun to appear. He realizes in that moment that he has won, that his actions have resulted in the rebirth of "the mutant race." I would love to see the scene where he apologizes to Mudbug's parents for insuring their son would live the rest of his life as a hideous freak, and justifies why this was a necessary sacrifice "for the good of the mutant race."
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