Scott tells Professor Xavier he’s just “here to listen”, until he discovers that Magneto has taken his friends and mentors by force and imprisoned him. Scott demands that Magneto release them. Magneto insists that no harm has come or will come to them if they do not retaliate, like Scott. Xavier attempts to communicate with Scott via telepathy. Magneto takes notice and puts Xavier into “decompression” as well. Xavier commands Logan to lose the battle with Sabertooth before losing consciousness.
Scott is angered and suspicious of Magneto, but his brother, Alex, tries to convince him that Magneto is not the enemy and he’s just here to “help” them attain full control of their powers.
Logan loses the battle on purpose, and finds out that Sabretooth has been taken away by a metal orb. Kitty, Kurt, Evan and Toad return to the Institute to find the place trashed and Storm missing. They find Mystique instead. Logan catches up to them soon after. They head out to Asteroid M.
Back on Asteroid M, Scott reflects on the past: The burning plane that crashed and killed their parents and how the brothers escaped with barely their lives on the two remaining parachutes, but got separated for ten years. Scott feels guilty about not being there for Alex throughout. Alex then talks about his surfacing mutant powers and that it wasn’t until Magneto that he understood what it was.
Magneto appears and brings them to the site of his genetic enhancer, which is going to help complete the evolution of their powers with the aid of the radiation from the gem of Cyttorak. Magneto also promised Scott that he would release his friends if Scott underwent the “transformation” to show them what Magneto “has to offer”. Scott is still doubtful, and Magneto demonstrates by “transforming” Sabretooth. Magneto revives the captured X-Men so they can witness Scott and Alex’s “transformation”. Xavier tries to warn Scott that the machine will “alter his mind” but he is too late.
Meanwhile, the rest of the X-Men together with Mystique and Toad arrive on Asteroid M. Since the craft is void of metal and he is unable to control it, Magneto sends the now transformed brothers to defend his stronghold. The craft crash lands towards them as they run to escape back into the tunnel. Jean uses her telekinesis to lift the brothers out of harm’s way. Logan releases the captured X-Men. He then takes on Sabretooth. Xavier commands Storm and Rogue to retrieve and prepare the X-Jet while he and Jean fetch Scott and Alex. The rest of the X-Men take on the Brotherhood. Mystique fights Magneto and is subsequently flung into the enhancer, and Magneto goes after her. As the place starts to crumble, most everyone abandons the fight in an attempt to escape from Asteroid M.
Jean and Xavier tend to Scott and Alex who are buried.
Scott: “You and the others, you’re ruining everything. This was our chance to unite, all of us.”
Jean: “Unite? And at what cost, Scott? Look what Magneto did to you!”
Scott: “He’s helped me, I’m evolved. No more training, no more hurdles, my powers are now at my mercy!”
Jean: “Yeah, and you blasted your friends with it. I mean how united is that?”
Alex: “You don’t understand. We are the future.”
Jean: “Really Scott? A...Are you the future? Because if you are, I don’t want any part of it.”
Xavier: “You’re right, mutants shouldn’t be divided. But we didn’t draw the line, Magneto did. It’s still there, you just crossed over it.”
Both brothers watch as Jean and Xavier walk away to the jet angered, hurt and disappointed. But Jean hadn’t given up hope that they would rejoin them. Unfortunately as they did, the bridge linking the asteroid to the jet collapsed. They fall into the Antarctic instead, hands linked, and with their powers they soften their landing. As the asteroid threatens to fall onto them and the jet, the brothers employ their powers at full force to destroy it. In the process, they are “detransformed”.
Jean: “Easy Scott, I’m here.”
Scott: “Jean, is everyone okay?”
Jean: “See for yourself.”
Jean comes over to reassure Scott and for the second time help replace his glasses. Scott apologises to everyone for making the wrong choices that got them into this mess. Even though they had lost all that they had previously gained, both brothers are thankful that they are reunited.
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