Having followed Moira’s request to come back to the manion, Cyclops is training in Danger Room to take his mind off things, completely forgotting to spend some quality time with Rachel, who is his future daughter, but has told Scott yet. Moira MacTaggert and Wolverine watch from the control room, and ask hto speak with him in private. Scott is told the reason Rachel feels so angsty : in her future, all her friends and family were slaughtered, and this could happen again in the present continuum.
Moira angrily points that she doesn't care about what might or might not happen : Charles Xavier is dying, after-effects of his mugging last Christmas and too much work are killing him slowly but surely. Nerves, heart, liver and other systems are failing. Moira isn't sure if he will live to see the birth of Scott's child. Moira also tells Scott that this must be the reason why he asked Magneto to join the team, probably to become Xavier's successor as headmaster of the school and mentor of the New Mutants; this last revelation infuriates Scott greatly.
In Washington, Val Cooper is returning home after doing some shopping; she is shocked to see an unwelcome guest in the person of Mystique, leader of the second Brotherhood of Evil Mutants. Val gets panicky, believing Mystique wants to kill her, but she is reassured by the blue-skinned mutant who offers her a glass of wine and takes on another appearance, that of President Reagan. Mystique offers Val the services of the Brotherhood as a government-sponsored team that could accomplish all the dirty work the Avengers and Fantastic Four wouldn't do, particularly where mutants are concerned. Val isn't buying, so Mystique confides that her team needs to adapt. Mutants are more and more threatened by homo sapiens' hostility; they'd rather become tools of the US government than being sentenced to life in prison by the federal court. She reminds Val of Quicksilver, the Scarlet Witch, Swordsman and Wonder Man : ex-villains who joined the Avengers. Now, it is the turn of the Brotherhood : Mystique and her team would obey exclusively to Val and to the President. The idea eventually seduces Val who sets a deal : amnisty for the Brotherhood's past crimes, but one slip even from only one of them, and the deal is over. Val adds that she want to test Mystique before talking to Reagan : the Brothehood is to capture and bring to trial...none other than Magneto, former founder-leader of the Brotherhood of Evil Mutants.
In St.Stephen Cemetery, where Jean Grey is buried, Rachel pays a visit to her defunct mother and tells her how she misses her and of how she is afraid to face her grand-parents in that timeline. She then goes to the home of John and Elaine Grey and waits till they have left, to enter the house. She has visions of Xavier and the X-Men telling John and Elaine Grey about the death of their daughter on the moon and Dark Phoenix being cast out of her home by her father. Suddenly, she remembers having been a baby in the arms of her mother, with her father worrying about the mutant situation turning to the worse. Back then Rachel was still happy, but years later, she was brainwashed into a mutant hound having to hunt others mutants. Rachel goes in her grandparents' bedroom and finds the Shi’Ar holempathic crystal containing the essence of Jean Grey. She touches it, and the sphere starts to glow. Rachel feels sorry that Jean Grey is remebered as a cxhaos-brinmgre and the evil Phoenix. Knowing that in her reality her mother did not give in to temptation Rachel vows to restore her reputation and she claims the name and power of Phoenix for herself. Around Rachel an energy bird appears. Rachel thinks that when Xavier dies, the X-men will have nobody popwerful enough to protect them from the likes of the Beyonder but her. She wants to follow her mother who saved the universe, both in her future, and in this reality by sacrificing herself. Rachel then collapses and the crystal breaks as it falls on the ground.
Back in Washington, Magneto and Kitty Pryde are attending the rememberance day at the National Holocaust Memorial; Kitty is speaking on behalf of her departed grandfather, Samuel Prydeman whose sister, her grandaunt Chava, lived in Warsaw before the war broke out. Magneto aks Kitty if she has a picture of her : turns out he knew a Chava Rosanoff in Auschwitz. Two elderly people rush to Magneto, amazed to see their old friend looking so healthy : Ruth and David Schulman had their life saved by Magneto after the fall of Warsaw and the deportation; they too knew Chava Rosanoff who died in Auschwitz, and confirm that she is the same Chava that Kitty was aking about. Kitty is surprised that Magneto could have been a hero, the master of magnetism retorts that in the camps heroism was to stay alive, to stay a human being in spite of everything the Nazis did to turn them into mindless slaves. Magneto points that is he is a hero for the same reasons than any death camp survivor.
Lee Forrester, who had been accompaning Kitty and Magnus, turns out to be Mystique in disguise: she asks Magneto if his friends are aware of his career as a murdereous super-villain. Mystique tells Magnus that she is now the head of the Freedom Force, a federal team whose mission is to put him under arrest for his crimes against mankind. Magneto encases her in a steel girder, but then the rest of Freedom Force show up : former Brotherhood members Destiny, Blob, Avalanche and Pyro, and a new inclusion by the name of Spiral. A battle royale between Magneto, the X-Men and the Freedom Force follows and concludes with Magnus being vainquished by Spiral with Mystique pointing a gun to his head. Cyclops and Wolverine save the day and are ready to evacuate their friends, but Magneto decides otherwise : he watched the panicked faces of his friends when he used his powers, exacly like his defunct wife Magda when he avenged their murdered daughter Anya so many years ago; he confides of how ashamed he is of the way earth looks liek because of his actions. Magnus feels no better than the Nazis and willingly turns himself in to Mystique's satisfation and the X-Men's amazement.