Following the battle against Proteus, the X-Men depart from Scotland. Final goodbyes are made as the powerless Banshee wants to remain at Muir Island with Moira MacTaggert, feeling that Moira needs him after her recent losses. Cyclops offers the Multiple Man to join the team, but Madrox declines, wishing to help Moira and Sean run the lab. Havok and Polaris do not wish to return to active duty either. They’re willing to help out if needed, but other than that they want to live a normal life. The two brothers hug and Cyclops tells Alex he hopes that he and Lorna will be happy. Alex hopes the same for his big brother and Jean.
During the flight, the atmosphere is relaxed, though Colossus silently agonizes over the ethics of his decision to slay Proteus.
In another jet, owned by the prestigious Hellfire Club, on a parallel course sits the mysterious Jason Wyngarde who once again reaches out to Jean Grey’s mind, giving her a taste of her innermost desires, slowly freeing negative part of her self.
For Phoenix once again the world turns topsy-turvy as she finds herself dressed in garments of the 18th century and on a ship en route to America with her lover Wyngarde. Overwhelmed by her passion for him she makes an excuse and heads for the deck. She fears she is losing her sanity. She had hoped that the timeslips were caused by Proteus’ reality-warping power, but clearly that is not the case. Could she be reliving the life of an ancestor’s of hers? Is anything impossible for the power of the Phoenix? Suppose she ever gets stuck in the past?
She is approached by the captain, who resembles Scott, and as soon as it began the illusion is over. Cyclops is worried about Jean acting kind of strange, but she brushes him off, doubting that anyone can help. Scott explains that while she was believed dead, he dated Colleen Wing, but it was not a serious relationship. Phoenix already knew as the thoughts emanated from the X-Men so strongly. Scott continues that Colleen is just a friend and that since Jean’s "death" he’s learned some things about himself: all his life growing up he lost people he loved, but losing Jean was the loss he couldn’t take: if he had allowed himself to grieve, it would have destroyed him, so part of his mind just shut itself down. He tells her that in the past he didn’t know what to say "I love you" truly meant, but now he has come to realize Jean means everything to him. They kiss passionately.
Upon returning to the mansion, the X-Men are in for another pleasant surprise: they find that Xavier has returned home (he had departed to the Shi‘Ar Empire). Like Jean Xavier had believed that the other X-Men had perished in Antarctica. Seeing that his children are alive and well, words fail him for joy.
The days that follow are quiet and a routine settles in again. Out on a romantic stroll with Scott Jean mentions that Xavier wants to runs some tests on her. She quietly thinks to herself that she’s caught some of his stray thoughts: she’s the reason he returned home. He’s worried about her ability to control Phoenix’s power.
Having returned to the mansion the couple wonders why things are so quiet. A moment later an angry Wolverine storms out of the Danger Room. Cyclops wants to know what his problem is and Logan furiously replies that he has had it with Xavier treating him like a kid or an amateur. "Wolverine don’t jump through hoops for nobody!" Scott has half-expected this problem. He joins the professor in the Observation Booth and they get into an argument over how to run the "new" team, as Xavier fails to acknowledge the progress that his students made while he was gone. Cyclops argues that while the originals were inexperienced teenagers, the new X-Men are not. When Cyclops tried to treat them like the old team, he failed. Xavier coolly replies that he is not Cyclops. Scott tries to stress the point that they are all individuals and have to be treated as such. Xavier bluntly tells him that this "anarchy" is a failure of leadership on Cyclops’ part. He should have taught these mutants how to be a team.. they are a team, Scott protests. Xavier cuts him off and sternly tells him that he hadn’t taught the new X-men in part because he trusted Cyclops to do so. That lapse will be speedily rectified.
An alarm interrupts the heated discussion. Cerebro has picked up two new mutant signatures, one in New York and one in Chicago, both displaying unknown powers. Xavier travels with Storm, Wolverine and Colossus to Chicago to make contact, while the others head to NY.
In their quarters in New York, the Hellfire Club overheard every word, as they have planted a bug in Xavier’s mansion. Jason Wyngarde smiles with amusement: "Poor Xavier. If only he knew…" He turns to the other men sitting in the shadows, addressing one of them as Shaw, and asking what their next move is. They’ll contact those mutants first, of course, and recruit them by hook or by crook, Shaw replies. Wnygarde warns them: the x-men are dangerous…. So are they, Shaw replies, as the X-Men will soon discover, won’t they? He addresses this question to a beautiful ice-cold blonde dressed in a white bodice and fur-trimmed coat. "As you say, Shaw," the White Queen replies, seemingly demure.
In Chicago Kitty Pryde is walking home from dance class.She is 13.5 years old, suffers repeatedly from migraines and her parents’ marriage is on the verge of a divorce Her Mom and Dad introduce her to Ms. Frost – the White Queen –, who represents a "very good school in Massachusetts." Kitty's Mom asks her why she's home early and Kitty tells her that she has another bad headache. Kitty goes up to her room to lie down as the migraine gets worse, then all of a sudden stops. She opens her eyes to realize that she's lying in the living room floor which is just below her room. Her parents and Ms. Frost walk in and she tells them that she tripped on the way to get some water. She runs back up to her room. The X-Men arrive, passing Ms. Frost on her way down the walk. Wolverine notices Frost, wondering why something about her makes him nervous.
Introductions are made and Kitty's parents send their daughter out with Storm, Wolverine and Colossus, while they talk to Xavier about enrolling Kitty in his school for gifted youngsters.
At the "Malt Shoppe" Storm and Kitty are on the way of becoming fast friends over some ice-cream. Wolverine in the meantime rifles through the adult magazine section of the shop and Colossus is quite embarrassed as a result. Curiously Kitty asks Ororo about her unusual looks: she’s never seen a black woman with blue eyes and white hair. Storm replies that she is one of a kind and so is Kitty. Because of her smarts? Kitty asks. Storm confides that they're really the X-Men. She is quite enchanted by the young girl’s energy and joy and wonders if she would have been the same at Kitty’s age if not for the accident that turned her into an orphan. She's about to tell Kitty that she's a mutant too when armed, armored Hellfire goons bust through the front of the shop. The X-Men fight, but find that the goons are prepared for her powers. Kitty accidentally phases through the back wall, then passes out.
Wolverine has an idea: each goon seems to be equipped to counter their specific powers. Why don’t they switch foes? They follow Wolverine’s idea and it proves to be successful as they dispatch of their foes. However Frost zaps them with a psi-bolt and has more troops load the unconscious mutants into a "hovercraft". They leave, but not before destroying the Malt Shoppe and all evidence that would point towards the Hellfire Club, including the three "armoured units". The three X-Men are stripped of their costumes and Emma Frost thinks that Kitty’s escape is not really important; they know where to find her.
Ironically Kitty phases into the back of the hovercraft unnoticed, hoping to somehow help the X-Men.