In the wake of Messiah CompleX, there are no X-Men and mutantkind still lies in ruin. With Magneto depowered and Xavier gravely injured, it seems their reign as the preeminent mutants has ended. But neither of these old soldiers is willing to go gentle into that good night, as Exodus learns when he squares off against Xavier on the psychic plane, with the fate of Professor X’s mind at stake.
As Professor X and Exodus face off against each other, Exodus tries throwing the Professor's past mistakes in his face to unbalance him. Omega Sentinel and Magneto look on at their physical forms as they battle. Magneto decides to do something and charges Exodus' body with a steel pipe. Exodus manages to send him flying back with a blast even though he is fighting on the astral plane. Omega Sentinel tells him not to forget how powerful Exodus is. Her readings are showing that they are at a full scale war against each other.
Exodus tries distorting Charles' memories to unnverve him. It doesn't really work. Finally Exodus pulls out scenes of the destruction of Genosha. Seeing the entire population be obliterated, brings Charles to his knees.
Across the world, Emma can sense two powerful telepaths fighting each other and recognizes one as the Professor. She tells Scott that he's alive out there somewhere.
Next is a scene of Charles training his new X-Men (that would perish on Karkoa). Moira says he's pushing them too hard but he says it's what they need. Then he watches as Krakoa wipes them all out. Then Jean (Phoenix) sacrificing herself on the moon in front of Scott. Colossus injecting himself with the Legacy Virus to cure the mutants. The scenes of his X-Men dying continue.
Exodus moves towards Charles asking if he yields to him. Charles looks up and tells him it stops now. He hits Exodus with a mindblast that sends him flying.
On the physical plane, Karima asks Charles if he's okay. He says he's fine but Magneto might have internal injuries. Exodus tries talking to Charles. He quickly stops him saying he could permanently shut his powers down mentally. Exodus tells the Professor that he didn't want to fight him. Everything he did, bringing him back and fighting him, was to ask him to lead the Acolytes. Mutantkind needs him. He proposes they find the Messiah baby and train her to fulfill her destiny.
Charles tells him he's a fool. He asks how he could want him to lead them after seeing all that have died under his care. He says his answer is no, he's leaving, and they shouldn't bother trying to stop him. Seeing the Acolytes downstairs, he recognizes Amelia but says he doesn't remember anything about her. He says since she wasn't in the images of those he's hurt, perhaps he's made her happy.
Outside he says goodbye to Magneto and Omega Sentinel. He says he wants to visit people that knew him to try to fill in the gaps in his memory. Before he leaves, Karima wants to know how he was able to beat Exodus when he was clearly beaten himself. He tells here that Exodus' judgment was wrong. He sought to break him down by throwing all his mistakes and guilt in his face. The mistake was those were the mistakes of Charles Xavier. He says the man that made the mistakes is dead. Now he has the chance to be someone better.
Epilogue One, Australia. Rogue pulls up to a gas station on a motor cycle. The attendant comments that she's headed into six hundred miles of desert and her bike could probably only cover two hundred and fifty. She goes anyway.
Epilogue Two, the Manhattan Hellfire Club. As Roberto Da Costa talks to the inner circle as they dine, a man asks to speak to Sabastian Shaw. He tells him that the machines in "room seventeen" were activated. At the room, he sees destruction and dead bodies. Shaw tells the man to seal the room, get rid of the bodies, and to bring him a file from his desk marked "Cronus."