With eyes full of sorrow, Professor Charles Xavier looks at a green glowing Shi’ar holempathic matrix crystal held in his fingertips. The first time he held one of these devices, an X-Man had fallen in battle. This second time is no different. The Shi’ar have used these small spheres to contain the essence and physical representation of a fallen warrior. This is an honor. The crystals are designed so no one was ever truly meant to be dead, but Xavier knows otherwise. Paraphrasing King Lear, “I know when one dead and when one lives…and Scott Summers is dead.”
The Professor begins to look back at the past of the X-Men. It started with only the first five X-Men: Iceman, the Beast, Angel, Marvel Girl, and Cyclops. Back then, the world was first starting to see the changes in evolution. The media called these people mutants and then began to attack them. Over time, new X-Men joined the fold, including Wolverine, Nightcrawler, Shadowcat, Colossus, Gambit, Rogue, and Marrow. Xavier knew that mutants such as them could easily have gone the path of being humanity’s predators, but did not. Humanity and mutant kind needed hope that would help both races, so Xavier started his Institute for Higher Learning to train mutants to help humanity. Knowing some would exploit mutants, Xavier founded the X-Men. Though the team only started with five members, it grew, including new teams such as X-Force and Generation X. Others were inspired to help unite both races such as Bishop, Cable, and X-Man. Thinking about Scott once more, Xavier thinks of the risks his students chose to take, but realizes that death will never get any easier. A new beginning is needed.
Shadowcat tells the Professor that the Shi’ar device is a keepsake, something to remember his students by on his journey. Xavier thanks Kitty as Colossus comes over to Xavier, still unsure as to why the Professor has to leave. Xavier turns to the group of mutant Skrulls who are preparing two ships. The Professor tells Peter that the Skrulls are now in his care and that they have no place on Earth, after how those before them gave Skrulls a bad reputation. Most of the Skrulls are children and they need a leader to find a new home in space. The Professor boards the ship and closes the door, leaving his two students behind. Kitty tells Peter that it is over as the Professor’s ship takes off from Muir Isle. Peter assures her that Xavier will be back, but Kitty believes that it is time that the X-Men follow their dreams. Kitty explains that she is 16 and that she wants a life beyond the X-Men and that now is the time to achieve those goals.
Aboard the ship, the Professor looks out a window with Fiz and another Skrull child. He knows that Kitty is angry and that she feels betrayed and abandoned. However, Xavier believes that she would do the same in his place.
At the Xavier Institute for Higher Learning in New York, the X-Men remaining at the mansion are all participating in a game of baseball. Storm and Archangel stand in the outfield while Psylocke, Wolverine, and Rogue cover the bases. Gambit is catcher and Marrow is at bat with Nightcrawler as the pitcher. Using her powers, Storm warms up the field so the team can play in the mid-winter. However, Storm is not giving her undivided attention the game. She remembers that baseball was her father’s favorite sport. He taught her how the play the game before he and her mother died. Storm thinks how Nightcrawler could easily make it into the Hall of Fame if mutants would be able to play. Storm feels uneasy, as if something is going to happen.
While she is thinking, Marrow hits the ball. It travels straight for the unsuspecting Storm’s head. Right before the ball would have made contact, Wolverine leaps in and “catches” the ball with a single claw by stabbing it in the middle. Storm apologizes to the others about her mental absence. She explains to the gathered team of how she is always expecting something to happen, even when the team finally gets a chance off. As Logan removes his adamantium claw from the ball, Storm tells the team that she thinks that their dual lives are always in turmoil and that the troubles of the past months will only lead to more dire challenges. Logan comforts Storm and tells her that the X-Men will find a way to win whatever challenge is thrown to them next.
On the Free Mutant Republic of Genosha, Magneto and his companion, Polaris, watch as a group of mutates battle against a group of human rebels. Magneto speaks to Lorna of his dream for a place where mutants could live in peace. That is what Genosha is for. The country was created by the exploitation of mutants by humans, but things have changed drastically. Polaris comments on how Magneto needs to get the local factions from killing each other. Magneto tells her that is where she comes in. Their powers are intertwined. While Magneto’s has weakened, Polaris could power him up. If the United Nations were to know of Magneto’s weakened condition, then they surely would attack him. As the two fly below to join the fight, Polaris can only think about the choice she made by coming with Magneto and wonders if she has just made a deal with the devil.
The National Reconnaissance Office of the National Security Agency is proud on being ahead in knowledge and power. Called the “Puzzle Palace” the agency cracks codes and runs surveillance. They can track anyone anywhere. Unfortunately for them, the mutant criminal Mystique developed most of it. As Special Agent Dale Fyre leaves the building no one notices an old woman shape shifting back into Mystique and then into the agent who just left. Mystique has created a horde of identities of the years. Recently, however, some of those identities have been compromised and she has come to clean up her tracks and find who is responsible for her recent misfortunes.
Back at Genosha, a heated debate is taking place at Magneto’s throne. Gathered are the Acolytes of Magneto. Sitting in Magneto’s throne is Fabian Cortez, who is telling his fellow Acolytes that Magneto is nothing without the power boosts he gives him. Magneto needs these power boosts to stay powerful, but it takes longer to recharge him every time. It is time to overthrow him. The Acolytes say he is talking treason, but Fabian asks them to consider what would happen if Magneto’s enemies ever found out about his weakness? Suddenly, Cortez is lifted from Magneto’s throne and tossed into a pillar. Magneto and Polaris have arrived. Magneto tells Cortez to worry about his own fate. Polaris is still thinking about her choice. Any blood Magneto sheds may be blamed on her. If she takes a stand against Magneto, would she have any chance to defeat him?
In Alaska, Jean Grey Summers is telepathically meditating on a mountainside. She died once but, like the Phoenix she is named after, she returned. She hopes the same for her presumed dead husband. Nate Grey, the X-Man, approaches quietly towards Jean, but he lights up the telepathic plane like a fireworks display even to a marginal telepath. Nate feels responsible for Scott’s death as Scott sacrificed his life to save him. Nate puts his hand on Jean’s shoulder. She turns around and immediately tells him not to blame himself for Cyclops’s death. Nate tells her that he was born to fight Apocalypse. Jean tells him that maybe he was meant to lose to him too, but Apocalypse did not consider that the team was ready to die for one another. That was the madman’s downfall. As Nate flies away, Jean telepathically tells X-Man that if he wants to honor Scott, then he should use his powers to earn himself the right to be called X-Man.
At a secret log cabin hideout, several villains have gathered: the Blob, Toad, Post, and Mimic. The latter three came as a request by the Blob. Blob has a presentation up which includes the floor plans for the Paradigm Micronics headquarters. Recently, the Deterrence Research Corporation has bought them out but PM was working on a weapon that DRC could care less about. Blob tells his companions about the prototype, as they all seem much interested now. The Blob has gathered all of them together to plan a heist, sell the goods, and become filthy rich.
On Genosha, Iceman and the Beast have traveled to the coast of the island nation on Iceman’s ice ramp from the African coast. Bobby wonders how he even got talked into this, but Beast tells him that he needed someone to sneak him in. Bobby sarcastically remarks that all they had to do was ice ramp a thousand miles while avoiding U.N. patrols to get into the headquarters of their arch-nemesis Magneto. Beast says it is for a good cause. Genosha has the highest population of mutants anywhere. That makes it a great place to research the Legacy Virus that is now dormant. Beast is worried that someone will find a way to reactivate the virus and begin the killing spree again.
Back at the Xavier Institute, the team has finished their game and settled for a lunch outside on a picnic table. Logan is sitting leisurely as the rest are discussing the disappearance of a Matisse from Warren’s penthouse last year. Gambit wonders why Warren is looking at him and Rogue reminds him that he is a thief. Gambit jokingly replies that he is more into Cézanne that a Matisse. Wolverine interrupts the conversation by telling all that they have company.
As a hologram appears, Logan says to trace the signal to its source but the holographic image tells them not to waste their time. The figure introduces himself as the High Evolutionary, caretaker of the world’s genetic potential. Telling the X-Men that mutantkind is too dangerous, the High Evolutionary says that the race must be eliminated. The Evolutionary continues by telling the mutants that they have the potential to supercede the human race, but their abilities give them too much of an advantage to determine the fate of all.
While Logan pokes his arm through the Evolutionary, Storm asks the man how many times his powers have led him astray and tells him that he has no right to pass judgment. The Evolutionary replies that he must do something. He does not want to harm them. He has designed an energy field that has the ability to neutralize the x-factor genome that makes them mutants. They would be reverted into the humans they could have been. Gambit reminds him that they are already human, while Rogue says that there is something they should do. Psylocke sarcastically remarks that this is another road paved with good intentions.
Nightcrawler realizes that the Evolutionary would not come if his plans were not already underway. The Evolutionary goes on and says that he has thought of every conceivable argument the mutants could bring up and he has prepared a rebuttal to all of them. If a few hundred mutants will die without their powers it is worth it to save billions of humans in the eyes of the High Evolutionary. It is a just act. The Evolutionary tells them about a world without Magneto and a world where they no longer have to struggle and free themselves from oppression that most have suffered since puberty or, like Nightcrawler, from birth.
Wolverine steps in and calls the Evolutionary by his last name, Whyndham. Logan says it is not that easy. Why does not the Evolutionary make everyone white to end racism? He could end homophobia by making the world straight. Logan makes a point that there are others more powerful who are not mutant: Dr. Doom, the Mandarin, the Hulk, and Thor. What about the Scarlet Witch, Firestar, Quicksilver, and the Beast? They are affiliated with the Avengers and Logan is sure their teammates will not take this lightly. The Evolutionary ignores the final plea and tells the X-Men that their fate is sealed and the Avengers would be fools to interfere.
With that, the Evolutionary begins the process. From the space station above, it begins. On Earth, mutants all over feel the effects. On Muir Isle, Colossus and Shadowcat convulse with what seems like pain. In Alaska, Phoenix falls to the ground that momentarily before she was levitating above. Elsewhere, Sunfire and X-Man also crash land. The techno-organic virus in his body suddenly attacks Cable. X-Force is gripped by the same force as well as Generation X. Sabra, Northstar, and Aurora are feeling the effects from wherever they are, as they scream out in pain.
At Genosha, Magneto does not go unaware as he catches Polaris who has fallen unconscious. With the Acolytes in agony Magneto realizes he can no longer feel the primal magnetic force of the Earth. Wondering who could have stripped them of their powers Magneto tries to fly away, only to fall to the ground along with his Acolytes. Magneto notices something else happening to the Acolytes. They are undergoing a biological reversion, becoming what they would have been if they were human. Magneto realizes that it won’t be long before his enemies learn that their powers are gone. The factions of the island will want to settle old scores, meaning they will want to kill Magneto!
At the NRO offices, Mystique is almost done with her scheme to hide her aliases. Needing one more minute, she quickly realizes she might as well have wished for the moon. As the biological reversion process hits her, she convulses onto the floor, reverting to her normal self. Her blue skin changes into white skin. When she opens her eyes again, she sees two guns aimed right at her head. At the villain hideout the men scream out in pain. Post’s rocky skin falls off to reveal a white-skinned man underneath. Mimic’s wings fall, as he can no longer sense any of the powers he has absorbed. The Blob’s extra fat goes away, but his extra skin does not, leaving his layers of skin to pile up on top of each other. However, the Toad has had a major change in the makeover department. No longer is he hunched over and ugly, now he can stand straight and admired his new handsome features.
On the Genoshan coast, Hank and Bobby are stranded. Hank tells Bobby that the effect is worldwide, according to his radio. Bobby is lying against a rock as the last of his ice form disappears. Hank only has a few patches of fur left. Bobby asks Hank if he has any ideas of what to do. Beast replies that this process is like no other, as it has actually tampered with the DNA in their bodies. Bobby begins to wonder who could be able to do this, but Hank figures from the devolving process that it is the High Evolutionary. However, the pattern is wrong, nothing like what the Evolutionary would be capable of doing. That means a second player. Beast has a suspicion, but it is too early to tell.
Back at Xavier’s mansion, the X-Men are no longer mutants. Storm puts her hand to her forehead, as she can no longer control the weather. Losing her powers is something she would not wish to be brought upon her enemies much less her friends. The team watches as Warren’s blue skin becomes white and his wings fall off and as Nightcrawler’s fur disappears along with his tail.
Still before the X-Men, the Evolutionary says that he knows the process must seem unfair and brutal, but he hopes they will accept it over time. Xavier’s dream has been fulfilled. Humanity is one. As the Evolutionary departs, he tells the team to begin their new lives.