Charles is talking to Moira MacTaggert about the new presence of mutants like himself. He tells her that he needs to find them. She has already catalogued about thirty gene samples from the hospital in Edinburgh. Charles tells her he'd like to be able to see the files but Moira says it's a matter of patient confidentiality. Charles insists that the research is more important. This is the birth of a new species and they will need their help. Moira is still a little hesitant but their conversation is interrupted when Bishop arrives. Charles recognizes that he shouldn't be there. Bishop says that Charles has killed them all and shoots him in the head. Charles falls back into the darkness of his mind as the words of the past X-Men are heard resonating within his mind.

In an unknown location, Exodus and his Acolytes stand around the unconscious body of Charles Xavier. Frenzy suggest that maybe it'd be better to simply let him die. Exodus reminds her that he did not ask for her opinion and that Xavier's mind is an asset the mutant race needs. He tells them he could repair Xavier's brain atom by atom but Xavier is somehow blocking his psychic probes and cannot figure out how damaged his mind is. Amelia says it's most likely due to his time fighting in Korea. He must have had to build up psychic barriers to block all of the death and destruction out. Exodus then figures he must completely wipe out Xavier's mind in order to rebuild it.

As he works, Omega Sentinel, who has been sustaining Xavier with life support systems, talks with Frenzy and Amelia. Karima seems to be free from Malice but the past few weeks are hazy. Amelia tells her what happened with everyone fighting over the mutant baby. After things were settled with Cable taking the baby away, they slipped away with the help of Tempo's time powers. It seems that Exodus chose them to help with Xavier and brought her along.

In Xavier's mind, he flashes back to his fist meeting with the original X-Men, fully dressed in their costumes. He shows them the Danger Room and puts them to the test. Later when he discusses the Danger Room with Moira, she is not too thrilled that Xavier feels the need to teach them to fight. He tells her that it is something they need to learn. Moira insists that not everyone has to fight. When she looks over Scott's file, she notices the initials, P.P.C. and questions it. Xavier tells her it means "Possible Prior Contatct." He feels this since Scott was at an orphanage but was given ruby quartz glasses that allowed him to control his optic beams. Moira feels that Xavier is bothered that someone else may have had a hand at shaping who one of his students is. Charles insists that is not the case then slips out of that memory.

Charles is now brain dead. Exodus says he is either catatonic or an amnesiac. He removed all his memories for his safety because his brain couldn't contain them anymore. Now his brain is refusing to take them back. He figures he just needs the right trigger to finish this.

Flashback to Scott and Xavier. Scott asks him how he resists the urge to play god. Then a flash to when Charles tells Scott he has to leave and wants him to lead the school and team. Scott doesn't feel he is ready. Charles tells him he is and that he's steered him away from his doubtful emotions. Scott is surprised and asks how exactly he's done this. Xavier says through teaching but Scott asks if he's ever gone into his head and moved things around. Xavier leaves that memory.

Exodus is back at Charles' side. With the continued failure to get his brain to accept the memories, he had no choice to seek help from Magneto, despite what he's done and what he is right now.

Overview

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.

Spoilers

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."