A theory states that, from energy, all things come to be, including matter and DNA. Human life is based on electromagnetic force. One week earlier, the man known as the High Evolutionary came to Earth to pass judgment on mutants. Using a device he created he reverted the DNA in the bodies of all mutants, effectively making them human.
He did this using an energy wave broadcast from a network of orbiting satellites around the Earth. He believed that these mutants had too much power and that stripping them of it was more important, to save the human race. Thinking himself as an ethical man, the Evolutionary had to step forward before humanity and the mutant race destroyed each other. Still, as an ethical man, he has been having second thoughts on his actions.
Up above in his laboratory in space, the High Evolutionary begins to believe that he has gone too far this time, that no one man has the right to dictate how a species should evolve. He believes he is now oppressing a whole entire race of people. Behind him, at a computer console, is an old man, Dr. Essex, his partner, who reminds the Evolutionary that eight billion human lives were saved compared to a handful of mutants who could destroy the planet. The two have just equalized the playing field.
The Evolutionary thanks Dr. Essex, telling him that he needed the words of praise after the X-Men could not believe what he was doing. The High Evolutionary comments on how Dr. Essex’s lifetime research on genetic mutation gives him a better point of view than others. In his younger days, Herbert Edgar Wyndham worked with Essex. When he began to evolve, he had to distance himself from all the people on Earth, making him lonely. What he wants most now is not a colleague in his research, but a friend. Going back to the other conversation, the Evolutionary says that more must be done to balance everything. His acts came at a cost. Essex agrees, saying that the cost is high for peace on Earth.
On Genosha, things have gotten worse for mutates on the island, who were already busy fighting a civil war. Now, the advantage is with the humans and their cybernetic enforcers, since mutates lost their powers. However, two X-Men have come to their rescue in the way they can: Bobby Drake and Hank McCoy, also known as Iceman and the Beast. The two were traveling with their new companions on Genosha when two cybernetic enforcers attacked.
Armed with only several guns and a group of wounded mutates, things are not looking in their favor. Suddenly, the cavalry arrives in the form of Magneto, Polaris, and the Acolytes, also armed with weapons but looking very rugged and weary. When the Civil War began on Genosha, mutates relied solely on their powers. With those powers gone, Magneto had to step in to save his people. Using guerilla warfare tactics, Magneto has come to save the day. Magneto blasts one of the enforcers away but the other one shoots him with a laser in the chest. Hank disposes of the last attacker as he and Bobby go to the aid of Magneto. Magneto tells them that he will be fine but Bobby reminds him that he is human now and that the insulated uniform he wears is the only reason he survived that blast.
Bobby tells Lorna that he is surprised that she is on Genosha with Magneto but Lorna tells Bobby that she thinks the same about him. Hearing reports that he and Hank were on the island, the group decided to rendezvous with them. Bobby apologizes, telling her that neither him not Hank can help much. Lorna tells him that the human magistrates of Genosha have been suppressing information, deciding instead to remove the mutants, quickly, once and for all. Magneto’s group has met up with Hank and Bobby to pool their resources together and find out who is responsible.
In the United Nations building in New York City, the Security Council has met, including Gabrielle Haller and a representative of Genosha, Alda Huxley, in attendance. These men and women have congregated to discuss Genosha and what to do with Magneto.
The Genoshan government has withheld any information but reports have begun to leak out that mutates have lost their powers. Gabrielle Haller believes that if mutates have lost their powers, then this is an opportune time to arrest Magneto for his crimes and gain control of Genosha. Ms. Huxley reminds Ms. Haller that the last time soldiers were sent in to get Magneto, not all came back. Ms. Haller does not respond as the other members of the committee agree. Instead, Haller begins to hope that the one man who could fix things would show up. The world needs Professor Charles Xavier and his X-Men. Gabrielle wonders where Xavier and his students are.
In Salem Center, the Xavier Institute for Higher Learning has been closed down until further notice. The mansion is quiet except for one room: the Danger Room. Inside the Danger Room, Kurt Wagner is running a practice session for himself. In the program, the now human Kurt is doing his best to follow his old self through a series of hoops, something he could easily have done if he had his powers.
However, Kurt no longer has the same muscles as his old self and he no longer has his abilities. Failing to catch a hoop after his hologram did, Kurt falls to the ground. Luckily, a safety net is deployed and he is caught safely. Leaving the net, Kurt finds Peter with him, a man who could once turn into living metal. Peter has begun to tap into his artistic side and has chosen it for his new career.
Peter tells Kurt that he knew he would find him in the Danger Room. Kurt does not know how to explain to Peter in ways he would understand. Peter had a choice between being Colossus or Peter. He had the choice to be metal or flesh. Kurt was born with blue fur and a tail, something that could not go away. After losing his powers, Kurt had to learn to walk again without a tail. He now has extra fingers, too. Kurt loved the way he was before and does not see his new humanity as a blessing. The two leave the Danger Room as Peter recommends that Kurt leave the mansion and takes some time off. Kurt, however, has only the mansion for a home, which is why he chose to maintain its facilities when the others left. Peter then tells Kurt that he was inspired by art in his time gone, now it is time for Kurt to go search for a new life, too.
Returning to the upper floors, Kurt says he will think about leaving when he smells the dinner Peter is cooking. Kurt makes a joke about leaving immediately if he knew Peter was cooking. Peter tells Kurt he was actually hoping to impress Kitty, who should be returning from her seminar. Kitty arrives as soon as Peter mentions her. Kitty has returned from school and was impressed but her new classmates are irritating and shallow, and interested only in boys, cars, and etc.
Peter cuts her off, reminding her that those topics are what she is supposed to be interested in. Peter tells he that she has piloted top-secret aircrafts and spaceships, met people from the future, battled demons, and saved to world over and over. Kitty then finishes his statement, telling Peter that she cannot mention any of this to anyone. Kitty is going through the mail when she finds a postcard from Warren and Betsy from St. Moritz. Looking at the picture of Warren and Betsy on the beach, Kitty comments that it looks like Warren has no regrets about losing his wings. Kurt, however, ponders over how an opportunity to pose on a beach can be worth more than the ability to fly.
In upstate New York is Camp America, a place for underprivileged children to get out to nature. Volunteers, including Marrow and Storm, former mutants and X-Men, run the camp. As the two women wave goodbye to the departing children, Storm asks Marrow if she is hungry but Marrow tells Storm that she has a date that night with Brad, a fellow councilor. Though Marrow’s bone structures are gone, she is attracted to the fact that Brad looks behind appearances.
Marrow and Brad leave as Storm remembers when she first met Marrow, who was violent. Since then, neither women has talked about the situation and their feelings, so Storm chose to take Marrow to Camp America so they could spend time together. Things have turned better than expected. Storm never realized that Marrow could be so happy and alive here, now that her powers are gone. The time Ororo has spent with Marrow has helped her keep control of her mind. Last time she lost her powers she was almost destroyed. The sound of thunder suddenly shocks Ororo, who at one time would have sensed that it was coming. Now she feels nothing and she thinks will never get used to felling so little.
On a subway platform stands Rogue, wearing a black suit with a skirt and glasses. In her right hand she is carrying a suitcase. At one time in her life she has to keep people away from her. Whoever she touched would be rendered unconscious as she absorbed their thoughts and powers. Now, she can touch anyone she wants. On the cramped subway, Rogue wonders how these people can go through life being squished in a small space touching one another. As a mutant, Rogue’s powers gave her personal space. Now she has none. Rogue begins to think of her time as a mutant, when she could fly through the air.
Enjoying herself, Rogue is suddenly thrust back into reality by a prison guard, who has just finished checking Rogue’s credentials. Rogue is now in a federal security prison. The guard, believing Rogue is a lawyer, calls Rogue over to into the room next to her. She tells Rogue that she has thirty minutes with her client, who is Raven Darkholme, a.k.a Mystique. Raven asks her what took so long while smoking a cigarette but Rogue cuts to the chase, telling Mystique that she has more problems. The Justice Department published a list of Mystique’s known false identities. As soon as it was released, her high priced legal teams bailed on her.
Mystique is outraged, saying that the lawyers accepted retainers but Rogue tells her that those powerful lawyers have other powerful lawyers, ready to defend them. Mystique, not caring anymore, tells Rogue that she must get her out of this prison. There are too many charges against her. She cannot stand being in one form for too long either. Rogue whispers to Raven, telling her that, without her powers, they have to stay within the legal system. Raven tells Rogue that there is no system for mutants and that she has to get her out immediately.
Elsewhere in the world is a community not marked on any map. No living beings have ever found this hidden civilization or suspect it exists. It is a lush jungle, but a massive fire is burning around the area.
Walking in a river, a woman is carrying a body of a girl. That girl is her daughter. Addressing her husband, called Hunter, the woman tells him that their daughter was underwater when their powers were lost. She was too far down to reach the surface and drowned. Hunter tells his wife, Domina, that the city is in ruins and that the majority of their people are dead. In one afternoon their entire world was destroyed. However, according to Domina, enough have survived. The Neo will be avenged. The flatscans have chosen to fight a war with them and they will lose.
Running down a dark alley is Jubilee, a member of Generation X until she lost her powers. Normally, she would be able to defeat the thugs after her but things are different now.
One of the thugs grabs Jubilee by her hair when, suddenly, someone in the shadows kicks him in the face. Jubilee turns around to see the man who saved her as he finishes off the thugs. The boys run away as Jubilee realizes her savior is Wolverine. However, Logan is a mess and is all bandaged up. When Jubilee questions what has happened to him, Wolverine tells her that he is in advanced stage of adamantium poisoning. The ironic part is that Apocalypse bonded it to his skeleton a week before the High Evolutionary took away their powers. Jubilee tells Logan that they have to tell the X-Men or Moira MacTaggert but Logan replies that Moira tried and failed. Jubilee wants to contact the High Evolutionary but Logan says he does not want to ruin things for Rogue and Marrow. Logan turns to leave and tells her to get back home and to stay out of trouble. He has unfinished business with a man named Creed.
In a dark dismal place is Moonstar of X-Force. She does not understand how she got into this forest or why she is wearing her original costume when she first joined the team that would become X-Force. She no longer has her powers to create mirages, yet somehow she is in this strange place following a voice calling her name. The voice is recognized by her to be of Cable’s. She confronts a creature that is fully techno-organic, a giant mechanical egg-looking structure. This structure, this entity is Cable.
He tells her to beware but Dani does not understand. Suddenly, she is snapped back to reality. With her, is fellow X-Force member Cannonball, ready to help as a friend. When Sam asks what happened, Dani tells him that she just had a vision on a psychic reality that is as substantial as the one they are on. This shows that her powers are not all gone, just evolving. They are evolving into something terrible.
On Genosha things are not any better. Underground are the mutates of Genosha, who are in terrible pain. Studying them is Hank McCoy, accompanied by Bobby Drake, Polaris, who is proping up Magneto. Hank tells all that all mutates are stuck in a mid transformation, one that is unnatural. The process that reversed their powers is mutating their mutated genes. However, it is only time until all life on earth is affected this bad, also.
Bobby tells Magneto that the mutates need help and Magneto asks where they should begin. All around them are men and women who are suffering because they are mutants. Hank tells Magneto that he needs rest but Magneto refuses to sleep until this crisis is over. The world needs to be fixed before it is too late for all. Walking outside, Magneto shows Hank and Bobby the last transport ship he has left. It has been repaired and ready to go, but it holds only two passengers. Bobby thinks Magneto wants to flee but Polaris tells Bobby that the ship was built for him and Hank.
Bobby, however, does not want to leave without Lorna. Polaris tells Bobby that she does not want to go; she is exactly where she wants to be. Hank asks Magneto what he wants them to do. Magneto tells him that he wants the two to get the X-Men and do what they always do: Huddle with their fellows, root out the source of the problem at hand… and put an immediate end to it, however, necessary. When Hank reminds Magneto that the regression wave is global, Magneto simply responds by saying that the X-Men must prove themselves without their powers.
Up in space, the High Evolutionary is monitoring his machines when he notices a stray signal from one of his stations. Seeing the Evolutionary perplexed, Dr. Essex asks what is wrong. The Evolutionary tells him not to worry but that there is a secondary transmission on their broadcast system originating from within their station. Suddenly, the Evolutionary screams out in pain as his suit is fried. Dr. Essex stands before the fallen Evolutionary and apologizes but he had not idea how else to stop him except to lock him in his containment suit.
Essex goes on to say that the second transmission was coming from him and that nothing seems to have changed since the two first met. The Evolutionary is still too easy with humanity and is softhearted. Essex begins to glow green as he tells the watching Evolutionary that the power he has does not belong to the weak, only to the strong that will not leave their goal. When the green glow is gone, Dr. Essex no longer stands above the fallen Evolutionary. Instead, stands Mr. Sinister.
Sinister tells the Evolutionary that a few final modifications will result in the satellites to not only affect the X-factor gene in mutants but all the DNA in every living thing on Earth. The Earth is now a giant experiment led by him to explore billions of different evolutionary paths for creatures in one generation. Sinister concludes by telling the Evolutionary that there is no one left to stop him.