Logan stares up at Phoenix with a goofy grin on his face. He calls out to her, but she’s apparently not listening. Instead, she telekinetically rips the ground out from beneath him and forms a wall of debris ready to drop down on the X-Men. Magneto and Storm are able to hold the wall back. Weapon X goes into berserker mode and threatens Sinister’s life for what he did to Jean. He’s stopped short, though, by Magneto’s magnetic powers, who tells him to wait. Logan says he wants Sinister to pay for what he did. As Magneto approaches Sinister he assures Logan that he will. First, however, Magneto wants to know why.
Sinister hears him and asks what he means. Magneto brings up the events of last year and how Sinister had left Apocalypse and was presumed dead. Magneto wants to know why he went to so much trouble if everyone thought he had died. Namely, why did Sinister blackmail him, brainwash some of his allies and resurrect Jean? Or most importantly, why is he following in Apocalypse’s footsteps when he was against him at the end?
Sinister finds Magneto’s comments hilarious and lets out a long laugh. He explains that he’s not trying to pick up where Apocalypse left off. What Apocalypse was doing was genocide and he didn’t believe in that. Instead, he was using Apocalypse to further his own ends. He needed Apocalypse to be able to run his experiments. His true goal was to find Mutant Alpha, the first mutant. Sinister tells Magneto his theory on Mutant Alpha. He believed that Mutant Alpha would always exist. Not necessarily the mutant itself, but the powers would be passed down from generation to generation. He spent most of his time searching for the genetic secrets that would complete the puzzle, which now has been finished.
Magneto incredulously asks if Jean is Mutant Alpha. Absolutely, Sinister tells him. She did stop a nuclear attack from happening and kept an entire timeline from being erased, after all. Magneto can’t believe this is what it’s all been about. Sinister tells him he now has the power to change the world, power that can be shared. Magneto can’t believe Sinister is offering some kind of partnership after all the turmoil he caused. Magneto tells Sinister he could never trust him. Sinister takes this opportunity to let Magneto know why he revealed himself to him so long ago. It was because he knew that Magneto would always be searching for him if there were even the slightest chance he could still be alive. Therefore, he wanted to keep him busy, keep him occupied until he was ready. “…to destroy you!”, he finishes with and the Sinister Six immediately go into attack mode.
“Lavalanche” sends some shockwaves that knock most of the X-Men back. Sonique lets loose with a scream that has everyone blocking their ears. Nightcrawler bamfs out of harm’s way with Gambit in-tow and reappears behind her. Gambit fires some projectiles at her and cuts her off. She turns around, but Nightcrawler has already teleported away. Silver Samurai shows up and smacks her across the midsection with his sword, knocking her over. He tells her she’s lucky he didn’t kill her. “Lavalanche” takes advantage of the situation and drives Samurai into the ground. Quicksilver joins the fray and repeatedly punches “Lavalanche” in the back. “Lavalanche” laughs and asks Quicksilver if that’s the best he can do. Rogue answers for him with an overhand right to the face, which knocks out some of “Lavalanche’s” teeth. He drops to the ground, unconscious.
Sinister tells Cloak to feed his darkness. Nightcrawler grabs Dazzler for her light powers to fend off Cloak. Gambit’s there as well, but it’s no use. Cloak swallows up all the light and then the three X-Men. Nightcrawler grabs them both and attempts to teleport them out, but Cloak closes his cape just in time, trapping them inside. Sinister giggles and says, “Three for the price of one!”
Meanwhile, Storm and Dagger are facing off. Storm manages to deflect all of her attacks. Psylocke comes over and tells Storm she would be a better opponent for Dagger and suggests she go after Cloak. Psylocke and Dagger put on a heck of an acrobatic show. They stop momentarily and Psylocke tells Dagger that she has her right where she wants. Magneto is behind Dagger and buries her amongst some of the debris.
Cloak sees this and freaks out. Sinister tries to keep him calm, but it’s no use. Cloak goes running over to where Dagger was buried at which point Storm skewers him with a lightning bolt. She tells him he has something that belongs to them and sure enough Nightcrawler and Dazzler come popping out. Storm tells Quicksilver to get over there quickly as Gambit is still missing. Quicksilver rushes over, but spots Soaron diving straight for his dad, who is helping Silver Samurai up from the ground. Quicksilver rushes over and deflects the attack, taking the full brunt of the force. Magneto is enraged and magnetically flings Samurai’s sword at Soaron, gutting him in midair. Soaron falls straight to the ground.
Sinister makes a remark about the Magneto of old and then tells Jean to repay the deed. Sunfire meets Jean in the air intent on protecting Magneto. They both attack with heat powers and at first come to a standstill. Jean begins to overpower Sunfire much to his surprise. His helmet starts fragmenting under the intense temperature.
Observing the arial battle from below, Logan tells Rogue to get him airborne. She does so and Logan attempts to break Jean of her brainwashing. He reminds her of the friendship they shared and tells her to snap out of it. Sunfire, his mask gone and looking fried tells them he can’t contain her any longer. Logan asks her to look at him and try to remember. Jean turns to face him and sheds a tear. Nightcrawler ‘ports in behind Jean with Psylocke and she uses the distraction to sink her telepathic blade into Jean’s temple. Jean screams out and Sunfire goes flying backwards, unconscious. He lands next to Sinister and lets loose with a huge fireball.
Jean is huddled over on the ground. She asks for Logan and he comes running over. He asks her if she is really Jean and then tells her how much he missed her. She apologizes to Logan in total disbelief. She says she remembers everything, her expression going from sadness to anger.
Jean telekinetically lifts Sinister’s charred, yet living body from the ground. She tells Sinister she should kill him for what he did to her, but she won’t. She tells Sinister that the others he’s wronged should also share in the joy of killing him. Sinister can’t believe it. Magneto stands at Jean’s side and helps to keep Sinister afloat with his own powers. Magneto tells Sinister that death would be too easy for him, but then admits that they’d all sleep a little better knowing he had been wiped from existence. Sinister tries to reason with Magneto, but he isn’t listening anymore. Instead, he tells Logan that it’s now time for Sinister to pay. Logan and Kirika unsheathe their claws, head over to Sinister’s floating body and slice and dice him.
Afterwards, Logan asks Magneto if he feels better. After losing his son, Quicksilver, Magneto says he doesn’t feel better about any of it. Nightcrawler brings up the loss of Gambit and apologizes for not being able to save him. Jean speaks up and tells them all she should be the one apologizing. If Sinister didn’t use her to brainwash the Sinister Six none of it would have happened. Magneto tells her she’s wrong and that he’s the one to blame. If he hadn’t kept silent about Sinister this whole debacle might have been avoided.
Jean suggests that they try to start over and attempt to put things right. Psylocke says she can start by reversing the brainwashing of the surviving Sinister Six members. Kirika hears this and asks Psylocke to start with her. Since she was once a victim of Sinister she wants to find the truth about her past and what her real memories are. Psylocke asks her if she’s sure, as the truth can be painful. Kirika assures her that she’s used to pain. Psylocke, satisfied, plunges her psychic blade into Kirika. Kirika collapses to the ground. Her memories flood back and she realizes that she’s not a clone and, in fact, is Logan’s daughter. He’s dumbfounded and asks who her mother is then. She tells him it’s Mariko Yoshida and then goes over and hugs him tight.
The X-Men are at the X-Cemetery and Sunspot’s, Shadowcat’s, Colossus’ and Iceman’s graves can be seen nearby. They’re paying their respects to Quicksilver and Gambit. Magneto creates two roses out of metal shards and places them on both of their gravestones. He kisses Quicksilver’s headstone and apologizes to him.
Rogue and Charles are sitting in the living room watching TV. They’re watching the news and the reporter is talking about how Magneto confessed to not being the one who averted the nuclear attack. That and then he turned himself in and was taken into custody. Rogue clutches her pillow tight.
At the aforementioned prison Magneto receives a visit from Jean Grey. He starts to ask her how she was able to get in, but Jean quickly reminds him of the advantages of being Mutant Alpha. She enters his cell and tells him that if he ever wants to leave to let her know. Magneto declines and tells her he wants to stand trial for his actions. Jean tells him she will respect his wishes.
Jean sits down next to him on the cot. Magneto asks her if she considered his request and Jean says she has and will take over as headmaster for the X-Men. He thanks her and asks about Logan’s status. She tells him Logan was a bit harder to convince, but will stay as well for the time being. Magneto expresses his appreciation for both of them. Jean tells him they owe him for saving their lives. Magneto balks at her comment, but she explains herself. If it wasn’t for Magneto forming the X-Men in the first place, they might not have survived to this day. And his actions after Apocalypse’s fall helped to ensure a save recovery for everyone.
Magneto tells her he saw Sabretooth and Blink in New Mexico. He can’t believe how sidetracked he got trying to get in good with the humans that he neglected his own people. Jean assures him she’ll do what she can to find them and any others they’ve lost track of, just like Magneto helped find her.
She gets up from the cot and walks out of Magneto’s cell. Magneto argues that he had nothing to do with finding her. Jean points out that he had Kirika locate Logan, an excellent tracker and Jean-devotee. If anyone would have found Jean it would have been him and Magneto willingly invited him back into the fold. Out of talking distance, Jean telepathically thanks him. Magneto smiles.
At the mansion, Logan, Kirika and Silver Samurai are saying their goodbyes. Logan tells his daughter about the last time he spoke with her mother, which was before the attack. He now thinks she might have been trying to tell him about his daughter. Kirika says she’ll ask her about it when she gets there. She asks her father if he’s sure he doesn’t want to go with her and Silver Samurai back to Japan. Logan thanks her, but tells her his place is with Jean at the Institute. Logan tells her to be careful during her trek to New Japan. Kirika assures him that she and her uncle can handle things, and Psylocke and Sunfire will be accompanying them as well. Logan takes a jab at Samurai saying that if he did a better job protecting Mariko, then she would never have been born. Samurai charges over to Logan, but Kirika keeps them apart. She tells them there’s no time for fighting and then hugs her dad goodbye. Kirika and Samurai walk out the door.
Logan stands with the door open watching them go. Jean shows up and asks him if he’s going to cry. Logan tells her that death didn’t improve her sense of humor. Rogue now enters and asks Jean how her husband is doing. Jean tells her he’s fine, a bit worn down, but fine. Charles, right behind Rogue in a Spider-Man outfit, shoots some webbing at Logan. Some more X-Men trickle in to the hallway. They wonder what’s going to happen to them, with Apocalypse and Sinister both dead. Jean reminds them that although things are pretty safe now, they won’t be for long. And until that day happens they wait and begin to dream again.