Far away from the Westchester mansion, anti-mutant riots, and the general havoc that Morph is causing, Scott and Jean are aboard a small schooner enjoying an idyllic honeymoon. They are heading towards an island that they thought was uninhabited.

Contrastingly, Beast is struggling to stay alive in the Danger Room. The setting that the intruder (Morph) put the Danger Room on is beyond mere practice. Beast is only able to escape by allowing the Danger Room to blow a hole in itself and retreating.

In a stolen cop car, Morph returns to the School for the Gifted. Once again, he begins to question his intentions. Why is he trying to kill the people who were once his friends? Mister Sinister appears from the surrounding forest and taunts, “Friends don’t abandon one another.” Reminded of his motivation, Morph is again focused upon retaliation, but Sinister claims Cyclops and Jean Grey are his.

Jean and Scott approach the island are greeted by Ruckus. He upends their sailboat, and the two X-Men wash ashore. There, the Nasty Boys do their best to apprehend them, and eventually Gorgeous George is able to slip on two of the mutant power-suppressing collars that were devised in Genosha. Powerless Cyclops demands to know his captor. Mister Sinister introduces himself to the pair.

Beast and Rogue visit Storm in the hospital. She is sleeping but according to her charts, she will make a full recovery. Rogue then accuses Beast of promising back up to them and then shirking. Beat honestly replies that he never heard about the mission. Rogue is unconvinced, but Beast guesses something is amiss. Before they can come to any real conclusions, they must leave Storm’s room when a night watchman spots them.

At a Friends of Humanity, meeting Graydon Creed is spouting another mutant-hating diatribe, but tonight he has something additional, a hostage. Jubilee is brought onstage with her hands tied. They are about to make an example of her when Wolverine crashed through the sky light. He makes short work of the F.O.H. goons, and they escape. When Wolverine asks why Jubilee was there, she replies that Storm told her to go.

At the mansion, Rogue continues to accuse Beast. They make enough noise that Gambit wakes up from his coma. Gambit and Rogue argue over who initiated the kiss that knocked him out. Rogue blames Gambit, but he insists that it was her suggestion. Professor Xavier (actually, Morph) enters the room and explains they may all be victims of a neural disrupter, thus the confusion. Then, Wolverine and Jubilee return.

Wolverine sniffs and realizes Morph is there. Xavier insists Wolverine is a victim of the neural disrupter, but when Morph stands to avoid Gambit’s charged card he is revealed as a fraud. Morph flees the room, as the X-Men are shocked by the actions of their comrade they presumed dead.

Morph attempts to steal the Blackbird, but he is stopped by Wolverine and Jubilee. Unphased Morph shifts into Logan. In the ensuing confusion, Jubilee blasts the real Wolverine, and Morph escapes. Beast, Gambit, and Rogue arrive in time to watch the jet disappear in the horizon.

Back at Sinister’s island, he explains his plot. He describes the decades he spent studying Jean and Scott, and how he will use their DNA to create a new, superior breed of mutants. He then draws genetic information from the both.

At the hospital, Jubilee gives the now-conscious Storm bittersweet news. Morph is alive, and he wants them dead.

Morph lands on Sinister’s island. He finds Jean and Scott restrained, powerless, and alone. First he taunts them with the idea of being left alone to die; and then he reveals that he was the minister at their service making their marriage null and void. Jean tries to justify Cyclops’s leadership decisions, but Morph could care less. He then prepares to shoot them, but Sinister stops him.

Morph is confused at the sight of Sinister. Why does Morph know him? Who is he and what is he to him? Sinister reminds him that after the sentinel attack, Sinister rebuilt his body and his psyche.

Rogue, Gambit, Beast, and Wolverine blast into Sinister’s lair. They have come to reclaim their own. They square off against the Nasty Boys. Wolverine brawls with Hairbag as Gambit disposes of Slab. Rogue handles Gorgeous George as Beast silences Ruckus (quoting Tennyson, no less).

Angrily Sinister assaults the X-Men. At Cyclops encouragement, Morph also attacks Sinister though unsuccessfully. Sinister repels all of them with powerful force blasts. Cyclops manages to muscle his way out of his confinements and frees himself and Jean. When Cyclops attacks Sinister, Sinister is shocked to find himself vulnerable to his optic blasts. He and the Nasty Boys retreat from Summers’ ire.

Morph also disappears while the X-Men were distracted with the villains. Wolverine declares that this time he will follow him.

Meanwhile in the South Pole, Magneto and Xavier meet both expecting last words from one another. They are surprised to find one another in good health. Xavier senses a trap, and then an avalanche traps them.