On a giant monitor in one of the basements of the Xavier Institute for Higher Learning, Hank McCoy gives his fellow X-Men a presentation on the current state of mutates on Genosha. On the monitor is a horrible picture of three mutates who are in agony as their bodies are evolving out of control. Hank tells the other X-Men that this is evolution gone wrong. Billions of different paths of evolution are being explored in one single generation. The DNA of mutates are reconfiguring themselves in order to create the perfect being for survival.
Hank continues on, telling the others that evolution is supposed to go slow. However, these mutates are only the beginning. Hank then tells the others that the human magistrates of Genosha have tried their best to suppress any information out so they can eliminate mutates quickly but he and Iceman were able to escape Genosha with the mutate pictures, thanks to Polaris and Magneto. Continuing with his presentation, Hank tells the others that, due to the unstable molecular structure of mutates, they are suffering the most but, soon, all life on Earth will be affected.
Assembled in front of him are Storm, Nightcrawler, Iceman, Rogue, Shadowcat, Marrow, Gambit, and Colossus. Storm points out that at one point evolution did go slowly but, as Colossus says, the High Evolutionary changed all of that. However, Colossus continues, he meant to help both mutants and humans, not destroy them, which means something has gone wrong. Hank puts on another picture on the monitor and shows the team that a system of satellites orbiting the Earth is responsible for the regression of mutants. Hank also took some time to compile a brief history of the High Evolutionary a.k.a. Herbert Edgar Wyndham.
One thing that Hank found most interesting was a photo of Wyndham’s early days at a university. Here he was mostly alone, but he did have one colleague and friend: a man named Essex. Given the field of study and the name, the X-Men realize that Essex is an alias and Mr. Sinister is behind this scheme. With their adversary’s identity revealed, the team begins to wonder what they are going to do. Storm suggests calling the Fantastic Four or Avengers but Hank believes they may be too involved in their own affairs at the moment. Hank also tells all that they must move fast for by the end of the week, everything will be mutating. Peter points out that even though they do not have their powers, they can still win. Nightcrawler agrees, saying the X-Men have a whole stockpile of recently required alien hardware. The rest of the team is in agreement.
Up above, in space, is the Evolutionary’s station, which has recently been taken over by Mr. Sinister. The Evolutionary has been sealed in a stasis tube until further notice. Sinister takes the time to tell Wyndham that it is his fault for all of this. Sinister tells him that his mistake was that he was limited from the beginning, always focusing on the subjects rather than the experiment. In the end he was all too human.
The Evolutionary tells Sinister that his only mistake was trusting Essex. He always suspected that something was wrong with Essex. Sinister replies, saying that Wyndham was too afraid to ask the questions he knew the answers to. However, a more disgusting error the Evolutionary made was having a horrible defense system in the station. Sinister knows that as soon as the mutation effect begins, the Fantastic Four, Avengers, and S.H.I.E.L.D. will come. Anticipating this, Sinister announces that he will create an army of Wyndham’s New Men to destroy them. The Evolutionary refuses to tell Sinister how to create them but Essex tells his captive that Wyndham shared enough secrets with Dr. Essex for him to deduce the rest of the process.
Back on Earth, Rogue is sitting on a couch using the phone. Calling the prison, she requests to talk to Raven Darkholme, using the cover name of Irene Adler, attorney-at-law. While she is on hold, Rogue thinks about all the charges that Mystique is facing, and how terrified her foster mother is. After only a week, Mystique is on the edge and Rogue is unsure of how to tell her that she cannot break her out.
Raven picks up the phone only to be told that something has come up and that she should not do anything. Outraged, Mystique yells at Rogue, mocking her by calling her “Ms. Adler,” and scolding her for calling and using the name of a woman both she and Rogue loved. She continues to yell, saying that Rogue has once again chosen her other family. Telling her to save the excuses, Mystique tells Rogue that this is the last time she will accept this betrayal as she slams the phone. Rogue is left crying on the other.
In the hangar, the rest of the team is busy working preparing their ship for space. Kitty points out the irony that they are fighting for a world that fears and hates them, yet now nobody hates them, because they are no longer mutants. Except, if they succeed in their mission, the world will hate them once again.
Nightcrawler, Shadowcat, Colossus, and Storm begin to discuss how being a mutant is their birthright and it’s who they are. No “cure” can stop them from being who they are. Colossus points out Marrow’s situation. She wants to keep her new humanity, yet she wants to save humanity at large, especially Brad, a boy she recently started dating. Storm says that Brad is the first boy to see Marrow for who she truly is, yet Storm admits that she is looking forward to this mission. She has yearned for an excuse to regain her powers. Sinister has given her that excuse.
Storm goes on to say that life, as a human, feels flat and dull when Wolverine, who just returned to the mansion, interrupts her. A shocked Storm tells Logan that they have been searching for him by calling his old contacts, but he had vanished. Logan tells her that he is dying of adamantium poisoning now that his healing factor is gone. Storm questions him on why he did not tell the team but Logan says that he did not want to ruin things for Marrow and Rogue if they went to stop the Evolutionary. However, he has been keeping an eye on the mansion and came when he noticed an increase in activity. He knows the X-Men need him and he has returned. Storm tells Wolverine that the team is preparing to assault the Evolutionary’s station but that Logan is too weak to go. Logan tells her that he is dying but that he is going to go down fighting.
On Genosha, the island is suffering from the continuing civil war. In their underground stronghold, Polaris is giving Magneto a report. The human magistrates have taken hold of the capital and have frozen all communications and transportation for 48 hours. This will keep mutates in while the military purges them. The mountain and coastal resistance are gone. According to her, the Acolytes could be the last mutants on the island.
Amelia Voght corrects her, telling them that they are ex-mutants. What is left of the island’s mutates are being destroyed by the accelerating evolution and the rest of them will not be safe much longer. Fabian Cortez agrees with Amelia. He tells Magneto that it was foolish of him to give the X-Men their only means of escape. The X-Men are also powerless to help Genosha and they are probably more than happy to see Magneto die. Magneto reminds Cortez that he is also useless to Genosha at the moment. He also reminds Cortez that the X-Men are hardly powerless and that they will find a way to succeed or die trying.
Back at the Institute, the X-Men blast off into space in a Skrull spaceship. Once they reach space, though, the X-Men feel a wave of nausea. Beast explains this to be caused by the G-Forces being acted upon them. That was something that their mutant bodies kept them immune to. As humans, they will now feel the sickness. Kitty voices her belief that the nausea is caused by the closeness to the satellites but Beast believes that it is highly unlikely. Hank has programmed the ship to take them to the Evolutionary’s station while staying far away from the satellites.
Unbeknownst to the team, Sinister is monitoring their conversation, to the horror of the Evolutionary. The X-Men’s arrival was already predicted by Sinister. He knew he would lose them in the chaos after the regression but now that he has found them he will put them to their ultimate test.
The team boards onto the side of the station and use their weapons to cut their way in. The team is now in and heavily armed. As soon as they enter, however, they are immediately shocked at the amount of sophisticated technology the Evolutionary has; they thought they had advanced hardware! Getting back to focus, the Beast tells the others that if they follow the generator conduits back to the main reactors, they should find Sinister and the Evolutionary. There, they will find the controls to the satellites.
While going down the halls, Gambit notices that the path leads to one direction that the X-Men must follow, like rats in a maze. That means one thing: a trap. A trap it is indeed as the X-Men are confronted by evolved versions of an owl, monkey, lizard, ameba, and other animals that are part of the New Men. The X-Men engage in battle under the watchful eye of Sinister. Sinister says that soon fights like these will occur over the world. Watching helplessly, the Evolutionary simply calls him mad. Ignoring him, Sinister states that soon the tide of the battle turns against the X-Men. As the others battle, Wolverine picks up the scent of Sinister and takes Storm and Shadowcat toward the scent. Kitty, however, is left wondering how Logan could have picked up his scent without his powers.
Back at the control room, Sinister tells the Evolutionary that evolution has already been interrupted by society. Now the world will see who would truly have won. Logan jumps from behind; telling Sinister it will not be him. Sinister says there is a chance he will not survive but neither will Wolverine.
Right when Logan is about to slice Sinister, an evolved rat attacks Wolverine. Shadowcat aims a gun at Sinister and demands he calls off his New Men but she does not heed a warning from Storm to watch her back and an ameba engulfs them both. Sinister tells them that he is always one step ahead. Logan finishes off the rat and attacks Sinister, slicing his chest. Sinister blasts Logan away, ripping off some of his skin, but not managing to kill him. Surprised, Sinister strikes again, not understanding how Logan is still alive. Logan, however, refuses to die as more of his skin and hair are burned off. Sinister blasts him again to the horror of Shadowcat.
Thinking to herself, Kitty realizes that nothing human could survive a blast like that. That’s when she realizes Logan’s healing factor is saving him. With a little struggle, Kitty phases out of the ameba. Turning to Storm, she tells her friend that the nausea they felt earlier was not the G-Force but the return of their powers as they went out of the range of the satellites. Sinister realizes his error. Though he is immune the mutation array, he never considered to have the station exposed to the field. Despite this, Sinister believes it is an error easily corrected.
Storm sends a small spark at Sinister; that is all she can muster. Sinister laughs at her, saying that she is done for but Logan comes from behind to strike the computer console. A giant explosion, sending the X-Men, flying rocks the station. After the smoke clears Storm tells Logan that it is all over. Shadowcat is holding a weak Logan. This is the closest he has come to death, but he will survive. The other X-Men arrive in time for Storm to announce that the satellite array is down.
Hank begins to treat Logan as the Evolutionary approaches them, telling the group that Sinister has escaped aboard their vessel. Storm tells the Evolutionary that Sinister would never have been a problem if it were not for him. Wyndham apologizes and offers a ride back to Earth but Kitty asks him how they can trust him ever again after what he has done, after he tried to “punish” them. Kitty mentions that this would have continued if Logan did not short circuit the control console. The Evolutionary corrects her, telling all that Logan only destroyed the console that held the Evolutionary captive. Wyndham himself destroyed his work, which he was doing for years. He is, after all, human.
He tells the team, who are looking down on Earth, that he never intended to “punish” them as Kitty said earlier. He then tells them that the global genetic order is returning to normal as they speak. Down on Earth, mutants all over the globe are regaining their powers.
On a city street, the Blob’s mass returns, shredding all his clothes. Out of rubble, Omega Red rises from a destroyed building. In Alaska, Jean’s telepathy returns in such a force that she screams out loud.
Elsewhere, on Earth, at a prison, two officers bid goodnight to each other as the female guard, Shirley, leaves for home. However, the guard is not real, as it is a shape-shifted Mystique. Thinking to herself, Mystique deems that prison has changed everything for her. Now freed, Mystique begins to conspire against all those who have betrayed her and who took advantage of her recent vulnerabilities.
On Genosha, the human factions turn around and flee as a re-powered Magneto and his Acolytes return with the vengeance. Magneto destroys all their tanks and gives them one last chance to retreat. Later that day, a group of mutates stand outside Magneto’s palace cheering their leader on for retaking the capital. Beside Magneto is Amelia Voght who tells Magneto that the human magistrates have been defeated and mutates across the island have returned to normal. Magneto tells her that this is only the beginning and tells her to go see to Cortez and the other Acolytes.
Entering his quarters, Magneto is confronted by…Magneto. The real Magneto tells the other that he is impressed by her work; he himself would never have given a better and stronger presence. The fake Magneto takes off her image inducer and reveals herself to be Polaris. Magneto tells her that they have much to explore as Lorna gives Magneto a power charge. The possibilities are truly endless now.
Back at the mansion, the X-Men have returned home. Logan, almost healed, stands with the rest of the team, happy to have their powers back.