After the injury he received Professor Xavier is taken home by his X-Men. They put him in his bed to get some rest and wonder how to continue without Xavier’s mental powers as they hear a car approaching. In the confusion they forgot that Marvel Girl’s parents mentioned to drop in for a short visit. Quickly the X-Men change into civilian clothes and greet their visitors. The students excuse Xavier and show the Greys around the mansion; the empty Danger Room is explained as a gym, whose new equipment will arrive soon.
As the tour continues Scott is accidentally locked in the Danger Room and automatically a training programm starts; only it is one designed for the Beast. Fortunately he is able to deal with any threat using his optical beams and after some time has passed the test ends. As the lock mechanism of the door opens Scott thinks that since the walls are soundproof Jean’s parents won’t have heard anything at all. The rest of the day passes without any problems and the Greys leave.
On his orbital headquarters Asteroid M Magneto and the Brotherhood try to locate the X-Men. Weeks of searching have given them no clues about their whereabouts, and the members ask Magneto why it is so important for him. He answers that as long as the X-Men exist they will intervene in his plans for mutantkind. But now Magneto has come up with a new plan to discover their headquarters.
At the mansion the X-Men tend to Xavier’s needs and watch TV. In a sports contest there is one combatant that wins every event by incredible jumps. The students conclude that this man is a mutant and as the audience of the sports event gets angry at the sportsman for cheating, the X-Men hurry to the stadium and rescue the him from the angry mob.
They plan to take him home but on the way the Beast recognizes something familiar about their new friend, he looks closer and pulls off a face mask, revealing the Toad underneath. A fight starts between the X-Men and the Brotherhood who had been following at a secure distance.
During the fight the Angel is caught and held with metal bands. Magneto, who now has a prisoner to interrogate, orders the Brotherhood to retreat, even though it means to leave the Toad behind. OnMagneto's space station the Angel is interrogated and as he refuses to give the mansion’s location away Magneto attempts to brainwash him.
The X-Men wonder what to do with their prisoner Toad, as he suddenly falls into some kind of trance. He is completly unaware of his surroundings and can only think about getting back to Magneto. Using a hidden communicator he calls down a capsule from the skies.
The X-Men decide to board it with him and they are all transported to Asteroid M, where the X-Men surprise the unsuspecting Brotherhood. Still this is Magneto’s base and he has designed a trap that would kill the X-Men with the simple push of one button. The Scarlet Witch interferes using a hex sphere on the control panel, as she can’t stand murder.
Magneto argues with the siblings about their loyalties giving the X-Men enough time to free the Angel and attack again. The fighting caused some damage among the asteroid and the station starts to break apart. Since Cyclops is in a section that already broke off, Iceman has to create an icetunnel through which Angel can retrieve his teammate. Before the full station is destroyed the X-Men use the capsule to get back to Earth. After they get out, the capsule is called back magnetically; obviously Magneto and his Brotherhood survived the explosion too.
Back at the mansion the X-Men want to fill in Xavier on the mission, but he reveals that he followed the mentally. He had never lost his powers but wanted to test how the X-Men would fare without him and they all passed graduation.