After the epic trial of Magneto in Paris, the X-Men and New Mutants are back at Xavier‘s School for Gifted Youngsters. The X-Men have a big surprise awaiting them as Madelyne Pryor gave birth to her baby while they were away. The X-Men all rejoice at the news and celebrate the arrival of the baby in their extended family, all except Cyclops who looks even more somber than usual. Nightcrawler makes a joke about what the boy will end up looking like with such a family and starts tickling Rachel who really hates being tickled. Madelyne asks Kitty Pryde to hold the baby, which freaks her greatly, but then she gets used to holding the baby and likes the feeling.
Maddie isolates herself with Storm. She tells Ororo she is feeling fine after giving birth alone in the kitchen but is mad at Scott for not being there when labor started: when he was in Paris, he never called her once although the other X-Men did; she doesn't reproach him for his absence, rather for his indifference. Storm retorts that Scott cares a lot about her but Madelyne needs proof for that.
In the other room Rachel is holding the baby in her arms and establishes a mindlink with him; she communicates to Kitty the baby's thoughts and both are in tears by the sheer beauty. Rachel promises her baby brother to always be there for him. Kitty says that sooner or later Rachel would have to tell Scott the truth, that she is his daughter from a future timeline.
Outside the mansion, Scott ponders on how happy he is to be a father and wishes his mentor was there to share his bliss, wondering if he should believe that Xavier handed the school to Magneto. After all they only have Magneto’s word for it.
Light-years away, the Starjammer is being hunted down by Shi'ar starships; on board the Starjammers celebrate the full recovery of Professor Xavier while examinating the full extent of the damages underwent by their starship. Waldo has bad news to tell: the ship’s integrity is down to 43%, most other systems are damaged too and especially the weapons are next to useless. Their ultra-light superstardrive is completely destroyed and they won't be able to bring Xavier back on earth before a very long time with the engines down and the trans-galactic doors guarded by the Shi'ars. Alone with Lilandra, Xavier ponders on his decision to entrust Magneto with his students and his school and can't help but worry about them. Lilandra retorts that all the regrets in the world won't change anything and reminds him that, at last, they are together.
At Xavier's, a disgruntled Sam Guthrie watches powerless as his computer crashes down, thus destroying his term paper which he had been working on for a month. In the garden the X-Men and New Mutants play base-ball. Nightcrawler wonders how Cyclops will be able to run the X-Men since he is now a family man, to which Wolverine retorts that the X-Men won't ask him to be their leader. Colossus sends the ball up in the air with Rogue catching it just as the presidential plane flies above the school; the astonished Ronald Reagan looks at Rogue, who blows him a kiss, and suggests to his staff not to talk the incident.
After the game ends, Kitty heads back home, exhausted, and finds her classmate Sam despairing in front of his computer; Kitty offers herhelp but soon learns to regret it: Sam did a messy job with entering so many data in the hardrive. As she exits the classroom, Storm delivers bad news: much to her dislike, Kitty has an appointment with the doctor. She will need to wear glasses.
In the attic, Scott and Madelyne are having a bone of contention about where Scott's loyalties really lie: with his wife or with the X-Men? Scott seriously believes his place is with the X-Men: Xavier isn't there anymore and Magneto isn't the right person to be trusted with the New Mutants' lives. Madelyne asks about her career, her private life: should she just forget about them? Scott naturally thought Madelyne would stop working and be a full-time housewife but gets his head bitten off when Madelyne yells that the baby is also Scott's son and that she is the only one in the room to earn money and to make a living. Scott retorts the X-Men do need him and that Storm being de-powered would be unable to run a super-hero team. Angry, Madelyne asks Scott if he really lacks self-confidence to only see himself as a super-hero and begins questioning his commitment to her and their baby. Scott doesn't answer anything. Ororo enters and offers Scott a hand-to-hand duel in the Danger Room to decide who should run the X-Men, unless he decides to leave with Madelyne. Scott accepts Ororo's offer and upsets his wife again.
In the Danger Room, Magneto is supervising the New Mutants' training session; Cyclops interrupts it by requesting the students to leave the room. Every student in the school gathers in the Danger Room's observatory to attend the leadership duel. The fight starts with Ororo proving Cyclops that she doesn't need any super-powers to be an efficent super-hero, as she uses her belt to make Cyclops topple, and then blocks his visor with his own arm, so that he can’t blast. Wolverine makes comment about Cyclops no longer being able to run the X-Men.
In the attic Madelyne wishes Scott could lose the duel, or rather that he decides to leave the X-Men of his own will. Only her first wish comes true: Cyclops loses the duel to Storm, as Ororo robs him off his visor. Having to keep his eyes closed Scott is helpless and admits defeat. Storm is now the official leader of the X-Men. Scott wonders if Madelyne will find in her heart to forgive him for the way he treated her.
The following night, Rachel visits the house of John and Elaine Grey while they are sleeping. When she was here last time, she accidentally broke the holoempathic crystal Jean’s parents got from the Shi’Ar. Rachel attempts to repair the crystal with her new found Phoenix powers. At the same time, the Watcher observes as some energy gathers in the spot wher Phoenix died on the moon and gets transported to earth in a tight beam. Having completed her task, Rachel leaves the Greys' house, the crystal now displays two images: Jean and Rachel, as she needed to add some of her own essence.