At the end of the last episode, Storm was about to open a door behind which several military troops were waiting or her. As she opens it, Wolverine stops her and tells her that he can smell gun-oil. Storm then uses her powers to blow them away, literally. Outside, a truckload of military troops have pulled up to the Agency. The X-Men engage them in battle, but Cyclops tells them not to hurt any ordinary humans. Gambit comments smartly that he should tell the normal humans not to harm them.

Back inside, in the guise of a commanding officer, Morph sends the men guarding the mutant registration files away. Storm assigns the computer to Beast, while she, Wolverine and Morph destroy the hard-files as well. In Detroit Michigan, Jubilee is shackled to a table. Henry Gyrich watches her on a TV screen, and speaks into a microphone. He asks her about The X-Men, but she says that she doesn’t know anything. Just then, Bolivar Trask, the man responsible for the Sentinels, walks in and berates Gyrich for bringing Jubilee there. During their discussion, it is revealed that they intend to use the Sentinels to capture all mutants. Just then Gyrich’s phone rings, and he is alerted to the situation at the Agency. He orders them eliminated.

Outside the Mutant Control Agency, the battle rages on, and Cyclops contacts Storm using their communicators mounted on their costumes. He tells Storm that he needs their back-up, and Storm tells him that they are coming out. They have all finished except for Beast, who quotes Archimedes and John Wesley while he installs a virus in the computer. However, Storm takes out the computer with an unexpected bolt of lightning, giving her apologies to Beast she states that they have no time for poetry. Upon hearing that Storm and the others are coming out, Cyclops orders everyone back to the blackbird.

Just as they are about to escape safely into the woods, several Sentinels appear in front of them. Wolverine instantly engages them in battle. Morph yells for him to look out as the Sentinel fires a blast from its hands. Back at the mansion, Jean is linked with Cerebro, she screams in agony and pulls the helmet from her head. The Professor asks her what’s wrong, and she states that it is Morph. The Professor puts on the helmet and says that he can’t sense Morph.

The Blackbird lands, Storm cries as she looks at an empty seat. Cyclops walks out of the jet, but Wolverine calls after him. Cyclops begins to say something, but Wolverine punches him in the stomach. Cyclops is about to return the favour when Jean stops them. Wolverine says angrily that Cyclops left them behind, and that Morph and Beast might still be alive. Jean places her hand on his chest and says that Beast is, when Wolverine asks about Morph, she simply shakes her head and she starts crying. Wolverine walks off and gets in his car, though not after slicing the roof off of Cyclops’ car.
Jean appears in the doorway and sates that what happened isn’t Cyclops’ fault. Wolverine drives off and she says solemnly that is wasn’t his fault either. As he drives, Wolverine thinks back to what happened.

Flashback:
Morph yells for Wolverine to look out as the Sentinel fires a bolt of energy from its hand. He pushes Wolverine out of the way and takes the brunt of the blast himself. Cyclops, Gambit and Beast run toward the Wolverine to try and help. But the Sentinel blasts Beast into an electric fence. Rogue tries to get to him but she is blasted out of the sky. More and more Sentinels surround the X-men until finally Cyclops agrees with Storm that they must retreat. Wolverine refuses and begins to walk off, but Rogue removes her gloves and grabs his arm. She absorbs enough of his strength to stop him, but not enough to hurt him.

(Present)
Wolverine swears to avenge Morph’s death. Back at the Agency, Beast lies unconscious on the ground, where several guards surround him. A Sentinel approaches, and commands the humans to stand aside, however, one of the guards refuses as the Sentinels were merely sent to help. Later, Beast hangs from the roof in a solitary confinement cell as Henry Gyrich attempts to question him. But Beast simply says: “Another time!” and returns to silence. Wolverine makes trouble in a nearby bar, and is saved by Cyclops when the people in the bar gang up on him. He is about to dismiss him, when Cyclops offers him the chance to take out the Sentinels’ home base. In Washington, the president has called Gyrich to come and see her. She exercises on a stair master as she tells him to stop all activity regarding the Sentinel Program. He angrily tosses a file into the hallway, when his phone rings. It’s Jubilees foster father. At Gyrich’s behest, he has called to inform him of Cyclops who has come to ask him and his wife about Jubilee. When he hears that Cyclops thinks the Sentinels kidnapped Jubilee, he informs Cyclops about his phone call to Gyrich and apologizes. Cyclops tells him that he has actually helped Jubilee.

Outside, a Sentinel arrives, it commands Cyclops to halt. Cyclops blasts off its arm, and it returns to base for repairs. Just as the X-Men had planned. Nearby, Storm states that she has the Sentinel on radar. The X-Men follow it in the Blackbird. The Sentinel flies to the same Facility where Jubilee is being held. It crashes through a skylight and collapses aboard a generator. The short circuit causes one of Jubilees shackles to open. She uses her powers to dispose of the rest. Next, she fires two focused blasts at a specific spot on the wall. Causing the metal to bend out of shape and eventually burst. She jumps through the hole and starts to run away, where shockingly two Sentinels stop her. Sitting on a beam above her, Cyclops tells her to get down. He takes out the Sentinels with his optic blast and Gambit destroys the other one by dropping several cards on him.

Rogue topples several Sentinels with super strength, while Storm casts lightning from the skies. Using their various catalogue of powers the X-Men eventually defeat all of the Sentinels. Jubilee bids her foster parents farewell, as she has been asked to live on at the school, and she has accepted. As she drives up in a cab, Cyclops asks Jean if she thinks he did the right thing regarding Beast and Morph. She states that he did what he had to do, as did they.