In the X-Mansion, repairs are beginning to take place after Deadpool’s assault and the freeing of the Juggernaut. Many of the students have been sent home temporarily, and the mansion seems empty.
Bobby Drake talks with Professor Xavier about the danger to students now that the X-Men’s enemies are taking the fight home. Xavier suggests that perhaps the formal combat team should be more separated from the school aspect of the X-Men. Perhaps X-Factor could take on more of the combat responsibilities. Bobby then switches topics to the source of mutant powers and how powers seem related to the self-image of the mutants involved. Worried about Rogue’s sanity, he pushes for the Professor to use this theory to help Rogue. Perhaps by helping her alter her self-image they can alter her powers to a state that is not slowly destroying her mind. He is frustrated with Professor Xavier’s response- that while they may understand the basic concept, the details of how self-image and mutant powers interact is still poorly understood and they cannot use unproven techniques on Rogue no matter how great her need. Behind Xavier’s usual imperturbable manner, the frustration at fraying ties with his sole remaining original student is beginning to build….
Nightcrawler pushes himself in the Danger Room, nearly flying as he spins from one item of gym equipment to the next and executing dizzying acrobatic maneuvers. He’s trying to share off the effects of Strucker’s death spores and clear his own head.
Elsewhere, Rogue confronts Wolverine during their morning training. She tells him she hates him for denying her the chance to destroy all of earth’s nuclear weapons by forcing her to kill him if she wanted to take his healing powers. She talks passionately about what it is like to grow up under the constant looming threat of nuclear war. Wolverine then reveals that he was trying to protect Rogue. He did not believe that mere temporary copied powers would be enough to save her life if she strained herself by pulling at every nuclear missile on Earth simultaneously with Cerebro. In his opinion, Magneto was willing to sacrifice her to see the event through and only by stealing Wolverine’s powers permanently would she be guaranteed to survive.
Scott Summers is meeting with the other members of X-Factor; Beast, Angel, and Ororo Munroe (who joined during his leave of absence). He thanks Hank and Warren for their patience in allowing his long leave of absence following Jean’s death and states that he is ready to rejoin the team. He then reveals that some of Jean’s Phoenix Force seems to have passed to him, radically changing the nature of his abilities and rendering them more unstable. Beast is overjoyed to see his old friend return, but Angel is more skeptical and asks that Scott be thoroughly examined, including a psychological examination. Before they can debate further, a massive explosion sends up a cloud of smoke in the center of New York.
Investigating, X-Factor tracks the explosion to the New York HQ of SHIELD where the Avengers base themselves. On the scene they find Loki, the Juggernaut, and the Absorbing Man standing over the defeated Avengers. The villains leave, tracked by Angel and Storm from the air. Beast provides medical attention to the downed Avengers and SHIELD agents, while Scott calls the X-Men to inform them what has happened. Scott explains things to Bobby, then realizes that his brother Alex Summers was also in the headquarters and runs off to find him leaving the phone dangling from its hook. Bobby runs to alert the Professor, only to find him slumped over in his office unconscious.
Then there is a knock at the mansion door. Samuel Guthrie and Autumn Rolfson show up at the Xavier Institute to kill the X-Men, with Guthrie politely requesting the X-Men come to fight outside in order to avoid further harm to the innocent students. Iceman, Nightcrawler, and Rogue emerge to meet the challenge. Magneto is left to take Xavier to safety, and Wolverine is absent. Confident that two mutants are no threat to them, Rogue challenges Guthrie about why he is willing to work for a monster like Apocalypse. He bitterly responds that after the X-Men left him to rot in the Raft, he concluded that everyone is equally terrible. Iceman is outraged that Autumn is blatantly ignoring the boundaries of Guthrie’s designated “fight area” when she attacks him.
Back in New York City, Loki turns and waves at Angel and Storm before teleporting his team away… to the Xavier Institute. Loki then announces that he’s done and departs, leaving the X-Men facing off against the combined might of Juggernaut and the Absorbing Man. Oh, and Guthrie is still there too. (Autumn had already been knocked out by an annoyed Iceman.) Despite the gravity of the threat Rogue is still reluctant to absorb more powers, knowing that each time she does she is slowly driving herself insane.
In New York, Scott is using telekinetic eye beams to lift rubble off Havok. Ozymandius appears, accompanied by a man in a wheelchair. They tell Scott he is needed and teleport him to the fight at the Xavier Institute. Scott assesses the situation and transform the ground to mud to bog down the Juggernaut, already trying to understand the situation to formulate plans to defeat the enemies. Then Apocalypse himself appears on the scene, and the X-Men understand that there will be no more intricate schemes, no more shadow games. He has decided to kill them all. A single blast of energy nearly does the job, but the X-Men pull through. Iceman puts up ice walls to hide behind. Magneto finally appears on the scene, but the the X-Men still have little hope against three of the mightiest beings in existence. And Guthrie was there too.
Giving up all hope of a tactical solution, Cyclops gives himself over to the Phoenix Force and unleashes a wide beam of burning red fire against all the enemies on the ground. He transforms the flying metal that Magneto brought into the battle into a shell of exotic unobtainium metal surrounding Absorbing Man, Magneto, and Apocalypse sufficient to hold them for a few moments. He calls a general retreat, and Magneto scoops everyone up on a flying disk of metal and carried them away while Scott holds the metal cocoons in place. Just as Apocalypse bursts free and is about to strike down Cyclops, Nightcrawler appears to teleport him away.
They regroup at the Massachusetts Academy and find it locked down. Professor Xavier remains stubbornly unconscious. Emma Frost emerges after some prodding and explains the the Hellfire Club is in the middle of a civil war, as those not controlled by Apocalypse fight those who serve him. Ozymandius teleports in with the man in the wheelchair, who he introduces as Frederick Slade the leader of Clan Akaba. Slade is possessor of two rare mutations- teleportation and empathy. It is the latter that is driving him to lead the Clan in rebellion against Apocalypse at this crucial juncture. Ozymandius believes that in the X-Men, he has finally found a force capable of fighting Apocalypse.
Other missing mutants such as Polaris and X-Factor arrive at the Academy as a rallying point as they are discussing what to do next. Then a radio broadcast interrupts. President Nixon is announcing the surrender of the nation to Apocalypse, who has escalated by arriving in Washington DC and conquering the United States. Apocalypse has ordered 200 Sentinels to attack Madagascar. Magneto, Storm, and many other mutants announce they will go to defend Madagascar. Angel leads a few to try and assist the rebel factions in the US government. Finally, Scott will lead a last desperate team to confront Apocalypse in DC.
Ozymandias and Frederick Slade tell the X-Men that Apocalypse is a psychopath, and that his weakness is that he fundamentally doesn’t understand people working together. This may be their only hope for victory…