Mr. Sinister and the Malice controlled Polaris stand in the ruins of the X-Mansion, the members of the X-Men and X-Factor defeated and Jean Grey his captive. The only person standing in their way is Longshot, who despite his doubts is able to create a distraction with his luck powers long enough for the Beast to recover and try to fight back. This in turn allows Cyclops to revive. Scott easily defeats Polaris and tries to turn his powers against Sinister, however Sinister has some form of control over him. When Rogue and Psylock revive and attempt to fight Mr. Sinister, Besty's mental attack is fended off, and when Rogue attempts to absorb his mind and powers, Sinister actually takes full control of her body.

During this brief possession, Cyclops sees Sinister standing over him and recalls a lost memory from his youth, where Mr. Sinister experimented on him as a young body. As Polaris tricks Havok into "helping" her only to bind him, Sinister explains that he had been manipulating Cyclops from the start, that he was in charge at the orphanage and stifled Scott's early powers and implanted false memories. As Havok is binded in metal by Polaris, he warns her that Inferno has changed him and he is no longer afraid of using his powers. Sinister explains that he also attempted to manipulate Jean Grey knowing that their combined DNA would create the ultimate mutant, however when Jean had seemingly died, he instead cloned Madelyne from Jean's DNA in order to fullfill this purpose. As Scott struggles to free himself, Colossus attempts to attack and is similarly held at bay by Polaris.

As Mr. Sinister continues to explain how he manipulated Scott at a young age, Psylock establishes a psylink between the scattered members of the X-Men and X-Factor, and they begin to formulate a counter attack plan. They note that Sinister appears to be keeping Scott under his power, as though he is afraid of Scott's powers, and figure that might be the key to defeating Mr. Sinister. Havok tells the others to let him deal with Scott and they launch their attack. As the X-Men pile on Mr. Sinister, Havok goes to his brother and while taunting him for being weak begins to bombard Scott with his atomic energy powers, charging Scott up with a massive amount of energy. As the X-Men fight on, Sabretooth comes out of the rubble of the X-Mansion prompting Wolverine to break off from the attack to deal with him, impaling his rival with his claws before returning to the battle. Storm uses her wind powers to sweet up Jean and uses rain to revive her as the others continue to pound Mr. Sinister with their mutant abilities -- however none seem to have an effect. Sinister manages to collect Jean back and begins kissing her, the final thing to push Scott over the edge.

When the Beast pulls Marvel Girl to safety, Scott breaks through the mental barriers and manages to blast Sinister with a full power optic blast, seemingly destroying his enemy. In the aftermath of the battle, Alex reports that Polaris escape and he and Scott make amends. With the battle over, the X-Men depart from X-Factors company, telling Scott that they will continue to fight Xavier's dreams in their own way and the two groups part as friends. Left in the rubble of Xavier's school Scott once more reflects on how he let his dead wife down so badly, however they all agree that they managed to save young Christopher and they will be committed to raising him together.

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