The X-Men have gone into hiding as the military enforces a nation wide search for all known mutants. Logan and Rogue are spotted in a convenience store in a remote and forested area and despite their efforts to shake the military off their tails, they track them to their mountainous hideout.
Meanwhile, Ororo and Hank appear at a White House hearings to try and persuade the senate to stop their pursuit of mutants. Juggernaut has also mysteriously escaped from his holding cell.
Back at the hideout, Scott is extremely pessimistic about the hearings, and Jean tries to talk him out of his “sulking”, reassuring him that she believes the professor will be alright. An excellent Scott and Jean bonding moment is once again rudely interrupted by Kurt who is trying to get a television reception.
Scott: “Thanks Jean, I don’t know how I’ll get through this without you.”
Kurt: (Teleports in and interrupts Scott and Jean.) “How’s the reception from here?”
Scott: “Lousy, like your timing.”
Scott, Jean, Kurt, Kitty, Bobby and Spyke are watching the hearings when Rogue and Logan crash in. The military choppers catch up soon after. Scott and Logan get into a confrontational spat. Logan insists on fighting them, but Scott stands by his hit and run tactics. Given their training, Scott feels that the X-Men are ready, and “very good”. Pissed off, Logan leaves the young X-Men to fend for themselves.
The X-Men take out the military choppers easily and escape in one of the choppers, leaving the soldiers unharmed. In the meantime, the White House is receiving live footage of destruction in the path of the Juggernaut and using that as evidence against Ororo and Hank’s testimonials that mutants.
Cyclops leads the team of young X-Men into battle with the Juggernaut on a dam. Working together, they attempt to stop the Juggernaut, as well as holding back the water leaking from the dam. Learning from their first encounter, the X-Men immediately go for his helmet as Iceman freezes the water in the dam.
Cyclops and the Juggernaut battle one on one, and while Cyclops’ uncontrolled optic blasts brings him down for a while, Cyclops weakens and is being subdued. Rogue then jumps at the chance and absorbs the Juggernaut’s power, using his own power against himself. Iceman freezes the Juggernaut as he is tossed into the river downstream. With their actions the X-Men clear their name. Trask, responsible for the Sentinel attacks, is also subsequently arrested.
Rogue having absorbed Juggernaut’s thoughts as well, uncovers the location of the captive Charles Xavier. The X-Men find the unconscious and trapped Professor in Juggernaut’s holding cell. Wolverine silently acknowledges that Cyclops has proved his point that the X-Men “aren’t kids anymore”. As the X-Men look forward to rebuilding their lives, Magneto plots his next move.