In Space on the blackbird. Rogue, Jean Grey and Professor X are trying to keep Wolverine in stable condition. A fatally injured, near-death Wolverine is strapped to a med-table, while it works on him. Bishop and Quicksilver are in the pilot seats of the blackbird trying to reenter the Earth's atmosphere. Gambit is in the back, working on the back-up controls of the blackbird. The Blackbird is escaping from Avalon and is hurling itself towards Earth at speeds and heat that the Blackbird cannot handle. Professor X and Jean enters Wolverine's subconscious to relieve some of Wolverine's psychic trauma.

Inside Wolverine's mind, Jean and the Professor see Logan's memories, Sabretooth, Lady Deathstrike, Weapon X wranglers, Wolverine's crucifixion, Magneto pulling the adamantium from Wolverine. Jean tells Professor X that being in his mind is a violation of Wolverine's privacy, and both exit his mind.

As the blackbird plummets into the Earth's atmosphere, the med-unit that Logan was on is snapped loose, and it bangs against the side of the jet, which awakens Wolverine. Professor X is about to give Wolverine meta-morphine for the pain, but Wolverine insists that he want to feel the pain, because when he dies he will be numb forever. Rogue and Jean reconnect the med-table, they see that Wolverine's healing factor is overloaded, wounds that were healing were breaking open again and Wolverine is burning up in a fever. Professor X calls Moira at the X-Mansion on the radio, he ask for help to stabilize Wolverine's vital signs. control panels explode and fail all over the jet from the stress of re-entry. The blackbird's wing cracks under the stress, Jean quickly uses her telekinetic power to hold the wind together, but she doesn’t know how long she can hold it.

X-Mansion, Moira tries to tell Professor X medical advice, while Jubilee, Iceman, Storm, Beast, Psylocke, Shadowcat, and Cyclops watch the monitor and worry for their fellow team members. Cyclops sees what is happening and remembers that last time this happen Jean turned into the phoenix.

In the blackbird, with Jean busy trying to hold the Blackbird together, Professor X is forced to reenter Wolverine's mind to flatten out brain-wave spikes that were proving to be dangerous to Wolverine.

Inside Wolverine's mind, Professor X witnesses Wolverine's inner struggles with himself, then Magneto disintegrates Logan. Professor X finds Logan again and grabs him to keep him away from the light, but the light pulls Logan forward. An angel descends from the light and kisses Logan on the forehead, Logan tells the Angel that he is ready to go, but the Angel pushes him away from the light.

In the Blackbird slows down enough that the wing will stay on, but the hatch door to the jet is beginning to shake itself apart, which would depressurize the cabin. Jean struggles to keep the hatch together with her telekinetic powers, but ask Professor X why he isn't in Wolverine's mind? Professor X tells Jean that their is nothing more he can do for Wolverine. A lighting bolt, from the storm outside, hits the blackbird, Jean loses her concentration and the hatch blows off, jean gets sucked out and hang on to the doorway for dear life. The Blackbird depressurizes, the other X-Men start to get sucked out the door, but Jean uses her powers to push them back to the controls. Jean tells them to get the blackbird under control and save yourselves.

In Wolverine's mind, Wolverine struggles against the wind that is blowing him back, but he sees someone’s hand and he struggles to reach out and grab it. Wolverine realizes that he is calling out for Jean and ask for Jean to bring him back. At the last minute, when the hand is about to disappear, Wolverine grabs on.

In the blackbird, Wolverine is pulling Jean back into the blackbird, Jean was shocked that Wolverine wasn't dead because his vital signs had flattened out. Jean thought Wolverine had come back to life just for her, but Wolverine tells Jean that it was her that pulled him out of death. They hold each other till the blackbird makes it back to the mansion.

Two weeks later at the X-Mansion, Danger room, the X-Men are practicing working as a team, Wolverine tries to join them, but Dr. Mora tells Wolverine that he shouldn't because he doesn’t have adamantium any more and he hasn't fully recovered from his wounds. Wolverine pushes her aside and says he has to prove that he deserves a place on the team. Jean tells Wolverine that he will always have a place with the X-Men. Wolverine tells Jean that he doesn’t deserve a spot on the team if he can't pull his own wait. Wolverine ask Professor X if he will give him a shot, Professor X starts the Danger room up. Professor X explains that these are real battle droids that he will fight, not the holographic ones the other X-Men fight. Wolverine dodges the attacking droids, then gets punches across the room. The X-men want to stop the simulation for Wolverine's sake, but Professor X says that Wolverine has to know what he is capable of. The droids begin to catch up to Wolverine, Professor X asks Logan if he wants the simulation stopped, Wolverine says no. Wolverine extends his claws, as the claws protrude through Wolverine's hands, blood burst out, Wolverine yells in pain. The X-Men are horrified to see that Wolverine's claws were bone. They quickly end the simulation to go tend to Wolverine.

Later outside the X-Mansion, Jubilee and Wolverine sit under a shade tree relaxing next to a pond.. Jubilee tells Logan that she is able to control her plasma-blast now, she can make a single blast or power up her blast strong enough to kill. Logan tells Jubilee that he doesn’t know much about himself, Logan doesn’t know why he can't remember having bone claws before the Weapon X project.

That night, Logan leaves a letter in Jubilee's room while she sleeps, then leaves one letter each for the rest of the X-Men. Jubilee wakes up and reads the letter. In the letter, Logan feels that he's not the best at what he does anymore, and therefore, he doesn’t deserve to be a part of the X-Men, Logan tells Jubilee to stay with Professor X because he will help her, just like he help him. As Wolverine drives off on his motorcycle he waves bye to Jubilee who waves back from her bedroom window.