After having just defeated Madelyne Pryor, Jean goes into a state of psychic attack, where she is struggling to deal with Madelyne's memories, as well as Sinster's control of Madelyne. Storm, Cyclops, Psylocke, and Wolverine enter her mind, and they all eventually drive Sinister out of her mind. They then decide to attack Sinister.
They go to Sinister's base, now Xavier's School. While searching, different groups are assaulted by Blockbuster, Sabretooth, and Malice/Polaris. They all are defeated, but at the last second Sinister causes an explosion to defeat them all. Only Longshot stands against Sinister and Malice.
Atop the Empire State Building, X-Factor and the X-Men begin to lick their wounds. The X-Men especially note that their demonized appearance is slow to dissipate and they wonder how much the Inferno has truly affected them all. Jean cries out and puts up a force globe to keep her friends away. Psylocke is able to get through, however, and pulls Storm, Cyclops, and Wolverine into Jean Grey's mind.
The group finds themselves on the Blue Area of the Moon. Cyclops can't believe that these are really Jean's memories, because this is the place where the Phoenix had died - Jean herself was already in suspended animation in her cocoon. Before they get any answers, a mysterious man begins to break up this memory.
The group then begins moving around Jean's mind and they find fragments of memories that should belong to Madelyne Pryor, not Jean. Psylocke begins to put together that the two women may have more in common than anyone could have ever guessed. The arrive at Xavier's school and meet Madelyne who immediately zaps Cyclops. Madelyne shifts into Jean, who claims that she is merged with Madelyne and is having a hard time controlling her thoughts. Psylocke tries to get Rogue in to help (she having to deal with merging personalities whenever her power is used) but the attempt is blocked. The mysterious man arrives yet again to destroy memories. Psylocke holds him off while Madelyne/Jean explains their backstory of how the man, Mr. Sinister, created Madelyne and how Madelyne just wants to give in and die, which would include allowing Mr. Sinister to continue shattering her memories (which now rest in Jean's mind, the two having merged at Madelyne's death). Mr. Sinister finally shakes Psylocke and asks Madelyne to finally yield to her fate. Jean takes over and lashes back, kicking Mr. Sinister out of her mind.
At his base, Mr. Sinister tells Polaris to alert his followers, as he is sure an attack is imminent.
Sure enough, Jean, Cyclops, Storm, Wolverine, and Angel arrive at Xavier's Mansion by air; Jean had picked up the location in her confrontation with Mr. Sinister. Rogue and Psylocke infiltrate the mansion on the ground. In the Morlock Tunnels, Colossus, Dazzler, Havok, and Iceman attempt to breach the mansion from below. Elsewhere, Beast introduces Ship to Longshot and Mr. and Mrs. Grey. Beast asks Longshot to stay while he goes to fight.
In the Morlock Tunnels, Blockbuster attacks by knocking Colossus across the tunnel. Iceman tries to counter but is ineffective. Dazzler also tries but gets snagged by Blockbuster, who is enhanced due to the lingering effects of the Inferno. Havok, uninhibited by his insecurities (also thanks to the Inferno) unleashes a blast and kills Blockbuster.
In the X-Mansion hangar, Sabretooth leaps out and pounces on Psylocke. Psylocke is too quick, however, and assaults Sabretooth's mind before he can do her any harm. Rogue is bummed that she didn't get the first crack at him.
In the mansion, Jean discovers that Mr. Sinister has gone through and smashed all of their things. The rest of the group joins Jean and gets attacked by Polaris. Polaris first attempts to kill Wolverine, but Jean uses her telekinesis to thwart the attack. Storm then grabs Polaris from behind and slams her down on the ground. Jean then binds Polaris. The rest of X-Factor and the X-Men arrive and Psylocke is tasked with entering Polaris's mind to learn the location of Mr. Sinister. Psylocke is to also see if she can separate Polaris from Malice. Polaris pleads to be spared, as she and Malice are now one and any attempt to separate them will kill her. Before anything can happen, however, an explosion renders everyone unconscious. Mr. Sinister steps from the ashes and claims Jean Grey as his own. He then commands Polaris (who had been protected by her bonds) to kill the others. The only person standing in her way, it seems, is Longshot.