The green shots continue to rain down on Wolverine. He turns to run, but doesn't get very far as the shots cover him in a green paralysis-gel, freezing him in place. The pod opens up, and the pilot, calling himself Trask, steps out. His men report that they've lost the other mutant to some magnetic interference, and Trask orders them to call off the search at get this one back to the facility.

Cut to Cerebro, where Jean says she's just lost Wolverine. Xavier tells her to keep trying, but Jean says that it's like he just disappeared, along with Sabretooth. Xavier expresses his frustration, saying that without Sabretooth they won't find Magneto. Jean gets defensive, saying that she isn't ready for this yet, but Xavier comforts her telling her it isn't her fault. He says that something unforseen must have happened, and they have to find out what that was.

Cut to the New York seweres, where Beast and Storm hunt for Logan. They find the shredded grate, realizing that Magneto must have used the grate to stop Wolverine from catching his old nemesis. An owl, listening overhead, flies off to the Brotherhood house, and morphs into Mystique. Rather than the typical speedy change that Mystique goes through, this one is slow and deliberate, almost as if she's concentrating on what she's just learned about the disappearance of Wolverine. She rushes downstairs, informing her young troops of the events, and says that there is clearly a larger strategy at work here.

Outside the Danger Room, mutants covered in orange paint sit sullenly, having been beaten in the training exercise. Rogue comments that Xavier can't possibly expect them to win in a fight like that. Inside, Cyclops leads the remaining mutants, but hesitates. Xavier barks at him to either leader or give Jean the responsibility. Cyclops commands the team to rush the Magneto robot. They do, Spyke kicking a rock down, knocking the robot's helmet off, triggering an explosion. The students get to safety, only to be bombarded with orange paint by the drones. Xavier commands all the X-Men into his planning room.

In the planning room, Xavier is overly critical of their performance, yelling at Cyclops for his poor strategy. Cyclops openly disagrees with Xavier's criticisms, saying that they shouldn't be expected to perform like regular soldiers when they haven't been trained in such a fashion, drawing even more criticism from the harsh Xavier. Xavier says he can't use the New Mutants because of their inexperience, and the older X-Men need more troops. Xavier introduces the newest recruits, the Brotherhood.

After some squabbling between the teams, Avalanche challenges Cyclops for leadership of the team, and Cyclops relinquishes, saying he's had enough of this. He storms away. Jean wants to go after him, but Xavier says that they don't have enough time.

In New York, an armored truck pulls into what appears to be an old, abandoned building. Inside, the drivers get out, and bring Wolverine out of the back end. Wolverine resists, knocking the two men across the room, until Trask activates the shackles, sending volts of electricity into Wolverine's wrists and ankles. Wolverine collapses to the ground in agony, and the men drag him to a freight elevator. On the way down, Wolverine comments that this must be a S.H.I.E.L.D. operation, and Trask says that he's no longer with the organization but stayed there long enough to learn of mutants. Wolverine realizes the man is a fanaticist, and asks what mutants ever did to him. Trask replies that humans are threatened by mutants, and they must rid the world of all mutants. Wolverine says that not all mutants are the same, that some "fight the good fight," and Trask says that this may be true but too many humans get caught in the crossfire. Trask says he has taken it upon himself to purify the world. Wolverine shows skepticism, pleasing Trask who says he'll wait and see if that's still there after an "experiment."

In Cerebro again, Jean shows Xavier that she's found Wolverine's signature, and Xavier orders the teams to assemble.

The Brotherhood board the X-Jet, and the X-Men board the Velocity. In the control room, Mystique sets the Mansion to Defcon 4. Xavier boards the Velocity, and the prepare for take-off. The two argue over whether or not to wait for Cyclops, but ultimately Xavier decides to leave without the commander of his team. The jets take off, just as the base goes to Defcon 4. Magma makes it out the front door just as it closes. Behind her, Cannonball hits diretly against the blast door, denting it. Boom-Boom pulls up in Lance's Jeep out front, as the base's defenses activate, targetting the young girl.

Boom-Boom blasts through the gates, driving in , destroying weaponry, and picks Magma up. The two drive off, getting away from the base.

On the hill, Scott sits alone on the hood of his Corvette, feeling sorry for himself as Boom-Boom and Magma drive up, and explain the situation. He realizes it's Defcon 4, and tells them to get in, and peels away. Boom-Boom explains that Mystique is back, and going over the current happenings Scott realizes that something very wrong is going on.

Wolverine is let out, into a makeshift arena, and, removing Wolverine's shackles, Trask explains to him that he is about to meet the savior of humanity, the Sentinel. Wolverine backs into a dark corner, just as a pair of glowing eyes, nearly 30 feet overhead, turns on in the same corner behind him. The robot steps out, nearly crushing Wolverine under its foot. The robot confirms that Wolverine is a mutant, and begins attacking, Trask looking on with pride. The Sentinel chases Wolverine across the arena, where Wolverine chops a crane down on the robot, and swings over to it, slashing at it with his claws, but not penetrating the coverings. The Sentinel tosses Wolverine into a few boxes, where Wolverine reorganizes himself and starts to climb the wall to get away. The Sentinel unleashes the arsenal in its chest, knocking Wolverine to the floor.

Scott's Corvette pulls up just below the cave exit for the X-Jet. The three mutants begin discussing how to get inside.

Inside, Cannonball continues to ram the blast door, nearly knocking himself out. Iceman tells him to stop, and to help him find the other New Mutants.

In the control room, the computer overrides the Defcon 4 command, and goes to self-destruct mode.

Over New York, five ominous steel spheres fly overhead, landing in front of an abandoned warehouse. They open simultaneously. First to emerge is Sabretooth, snarling and angry as ever. Second is a brown-haired man holding a staff and a deck of playing cards and ignites a card with kinetic energy. Fans will recognize him as Remy LeBeau, the "ragin' Cajun" known as Gambit. From the next pod leaps a great wall of flames, forming into a face. At the bottom of this is a red-haired main dressed in a flame-proof suit and wearing flamethrowers. It is John "Pyro" Allerdyce. A tall, muscular man with Slavic features emerges from the end pod. Suddenly, his skin begins to turn to steel, revealing that this is Piotr Rasputin, the man known as Colossus. Finally, Magneto emerges from the center pod, his team prepared to fight against the duel threat of the X-Men and the Brotherhood.

Back in the arean, the Sentinel stalks over to the rubble burying Wolverine, and, picking him up, prepares to destroy the mutant.