Since her return, night after night, Jean relieves her nightmares of the fateful day the Phoenix force appeared to her as she was dying in the space shuttle. The Phoenix put her in a cocoon to heal, offering her the “gift of life” in exchange for the chance to experience human life and emotions as Jean Grey. The Phoenix went on to take away her “hopes” “dreams” and “memories” while she lay “in a state of living death”.
Jean despaired at all the changes that had taken place. Charles Xavier was gone and Magneto had taken his place at the Institute. The original X-Men had broken away to form their own team, disguised as mutant hunters in order to “protect and train” their own. Unable to sleep, Jean wanders around the new X-Factor base, feeling lost and trying to figure out how she fits back into the world.
Meanwhile, in another part of the building, Warren is trying to convince Scott to come clean with the truth before it hurts: Telling Jean that during her supposed death he married Madelyne Pryor and had a son; and telling Maddie that he had left her and his son to form X-Factor with his old flame, the original Jean Grey. Warren storms off to handle “administrative” duties after Scott tells him off, saying Warren will never understand the dilemma he is in.
In the city, Hank and Bobby are out apartment hunting, not wishing to be confined to the current X-Factor base. They also pay a visit to an old friend and former girlfriend of Hank’s, Vera. Unknown to them, they are being watched by a mutant known as Tower.
Later that day, Rusty’s training session begins, with Marvel Girl as his tutor. Rusty gets frustrated with his inability to control his powers and leaves his session abruptly. Cyclops tells her to let him go and not to put too much pressure on him as these things take time.
Jean tries to seize the moment that they’re alone together to find out what Scott’s been hiding from her that’s making him behave so cold and distant towards her. Scott evades her questions and goes to check on Rusty.
With the ability to shrink and grow, Tower sneaks into Vera’s apartment building and springs an attack on Hank, Bobby and Vera, resulting in the kidnap of Hank.
Scott finally decides to take Warren’s advice and call Madelyne, only to find her number disconnected. X-Factor is then called to assemble by Angel with reports of a mutant sighting. At the scene of Vera’s apartment, a shaken Bobby tells them a mutant has kidnapped Hank.
Tower had taken Hank to Atlanta’s Ryan Bio-Chemical Laboratories, a research facility patronised by the government. Hank is taken to a lab below the surface, where he recognises the mastermind behind his capture, a former co-worker named Carl Maddicks. Carl seeks Hank’s knowledge about the “chemical source” that causes mutation in the human genome. Hank warns Carl that his “associates” will come looking for him once they find out he has gone missing. To throw X-Factor off, Carl tips them off as to the whereabouts of Tower, despite having paid him his dues.
With that, X-Factor make their way to Atlanta. Jean has reservations that they are walking into a trap.
Next: X-Factor #3