Magneto and Jubilee have brought the unconscious Logan to a secret mansion at the coast of India. Once inside, Magneto feels like this is just another stop on his long journey, and Jubilee fears that she’s going to lose Logan now as well, seeing how she is one of the few survivors of the once mighty team of X-Men. Jubilee asks Magneto to tell her that they are there for a reason. Magneto understands Jubilee’s distrust, but wants to try it for Wolverine’s sake. He reminds Jubilee to forget the past she has with the woman they are about to see, as it wouldn’t be the first time that they would have to turn to an unexpected candidate for help.
They arrive in a big room, with a background of the 18th century. Their host is dressed the part, and Jubilee recognizes her as… Emma Frost! Emma welcomes them both, but Magneto tells her to cut out the illusion, as he doesn’t like it. Emma agrees and, with one move of her hand, the room changes in a big control room, with a lot of computer panels and viewing screens. From there, Jubilee is aware, Emma can witness everything what’s going on in the bad society of today.
Magneto cuts to the chase, mentioning that they don’t have time for games. He is fully aware that this cut-off place has made Emma gone totally crazy. Emma doesn’t agree, as everyone handles the crisis on their own way, and this is just hers. Emma greets Jubilee, noticing that she has gotten a lot older since the last time she saw her. Jubilee doesn’t care, and tells Emma that they need her help to restore Wolverine.
Emma hopes that she doesn’t have to help for free. She knows that the world has changed, and that the dreams from their youth didn’t come true, and she has learned that she can only trust on herself to survive. She is full aware that a lot of people like her telepathic powers, and Emma wants to be paid for her services. Magneto understands that everyone has a price, and asks Emma to name hers. Emma smiles, realizing that they really need her help this time, and that even the savior of all mutants has come to her. That is already payment enough, she smiles.
Magneto gently drops Logan in a chair. Emma goes over to him, but concludes that the situation is hopeless. Emma begs Emma to forget their differences, as this is important. Emma wished she could but explains to Jubilee that, when she and the others walked out on her, a little more than just a dream died in her. Magneto has had enough of the talk. Emma understands, and tries to enter Logan’s mind. Jubilee warns her to be careful, as, when they found Logan in Moscow, he nearly tried to kill her. Emma tells Jubilee to be quiet, as she needs her concentration.
Soon afterwards, Emma succeeds. Logan wakes up, but the only two things he feels are confusion, and rage! He recognizes Magneto and, since they have unfinished business, Logan snikts his claws open and tries to attack him. But Jubilee holds him back, explaining that Magneto isn’t the enemy this time. Logan recognizes Jubilee and calms down, remembering that it has been a long time since they last saw each other. For a moment, there is a total silence, but not for long. Jubilee and Logan hug.
Logan wants to know what’s going on. The last thing he remembers is that he went to Moscow to find Amiko. Magneto mentions that they’ve got little time to spare, and cuts to the chase. He explains to Logan that the world has to deal with a lot of natural disasters. But, Magneto has discovered that those disasters are anything but natural. And they need Logan’s help to end them. Logan understands and agrees to help, but wants to hear one good reason why he should help Magneto. Because, Magneto says with a serious look in his face, they have something which he thought he had lost: his daughter, Wanda!
At the same time, but on another part of the world, Wanda is being held prisoner inside the Hoover Dam. There, she has been put unconscious inside a powerful machine, which manipulates her in using her powers to manipulate nature. But, in between, she mourns the death of her brother Pietro, who’s been gone for a few years now, and also her long lost mother, who has been dead a whole lot longer.
From a balcony, Shinobi Shaw and the former X-Man Psylocke observe Wanda, and find their plan to be brilliant and simple. They are confident that chaos will soon rule everywhere, and that anarchy shall conquer the entire planet. And, Shinobi adds, the old world order will make way for a new order, with him as the Black King and with Betsy as his Red Queen. East and West gathered as one. Shinobi smiles, as not even his father had the courage to try something like this. Sebastian was always trying to smooth talk the other politicians, while the world lied with the palm of his hand.
Suddenly, Betsy gets a headache! She senses that Wolverine woke up again, and that Emma is responsible for it. Shaw finds that interesting and suggests that they send out Midnight to finish of Logan once and for all, as they can’t allow Logan for coming so close. And so, deep within the catacombs of the Dam, Betsy goes to find Midnight, and explains her mission to the woman. Midnight hasn’t a problem with this, not even seeing her past with Logan, as cheat means so little nowadays.
Betsy remains silent, and only remembers how her former lover, the X-Men Archangel, was literally burned to death in front of her. Betsy smiles that they all had their defeats, and asks Midnight if she agrees with the mission. Midnight promises that Betsy’s got nothing to worry about, as she has been waiting for years for a chance like this, and will find Logan.
At the same time in Portland, Oregon, former police officer Charlotte Jones walks over to an abandoned house, remembering she is now the leader of an underground rebel group, which is just her way to help out, recalling it was an easy choice to choose either this, or having kids. Charlotte walks around a few times hoping not to get noticed, before she eventually enters the building.
Charlotte goes deeper inside the dark building, and meets up with Synch and Leech! They hug. Synch wants to know if Charlotte has heard anything from the X-Men yet. Nothing new, unfortunately. They are still trapped in the concentration camp in Manhattan. That’s all Charlotte knows.
They all try to see what the X-Men would be like now, sitting in those camps. Leech hates the fact that they had to leave the X-Men alone like that. Synch promises to go try and free them once Jubilee has returned. He recalls her having made a deal with Magneto, who promised to help them in return for finding Logan. Charlotte isn’t sure Magneto will keep his word, if Wolverine doesn’t kill him first. She is aware that all the Thunderbolt agents are after Magneto, and worries what’s going to happen if they recognize him. Suddenly, the roof above them breaks open! Charlotte doesn’t understand, as she thought she had been careful enough, and refuses to get arrested now!
Some time later, Logan has brought Jubilee and Magneto to the remains of Department H in Canada. The place brings up a lot of both good and bad memories back to Logan. Jubilee asks Logan how things are with Amiko now, and Magneto asks him if that’s his daughter. Logan says, in a way, Amiko is his daughter. He explains that, when Amiko was six years old, he promised he would take care of her. She was tough, but too young to stay with Logan and his adventurous life. So she left her with Yukio and the Silver Samurai, who promised Logan they would protect her, and admits that Amiko would have a better life with then than she would with him.
But things went wrong, like so many. There was an accident, he recalls. Amiko died before her thirteenth birthday. Except… her body was never found. Logan built a tombstone for her and visited, but was always suspicious. And a couple of months ago, Logan started getting evidence that Amiko was still alive, in the form of photo’s of Amiko what she would look like today. So, he came to Moscow looking for her, but now Logan fears that might have been a trap. Logan stops talking, and catches a scent he recognizes. They’re there.
James Hudson and his soldiers step out of the shadows, with their guns ready! James recognizes Logan, and wants to know what he’s doing on Magneto’s side. Logan nods that times change, and asks James to put the guns down. Logan reveals that he’s here to pick up something he left here a long time ago. They move deeper within the building, and Jubilee recognizes the piece Logan is talking about. Now this is history, Jubilee jokes. Logan suggests to the others that they just climb aboard, and do so. As they do, nobody notices that Midnight is watching them in the shadows above.
And so, the Blackbird departs! Everything from the controls seems to work, and Jubilee sets course to the South-West, like Magneto wants. Magneto finds it ironic that he now sits in Xavier’s plane. He wishes that if only his old friend would have listened to him, as then everything might have turned out differently. Magneto is confident that together, they could have defeated the Sentinels before they ever could gain control. Wolverine mocks that Magneto is right. He would have saved them… like he did back in Genosha!
Magneto angrily powers up, defending that Wolverine doesn’t know what happened there. Logan doesn’t care. After all, he isn’t doing this for Magneto, but for Wanda. So he suggests that Magneto shuts up. He does. Soon afterwards, they arrive at Hoover Dam. Inside, Shaw’s guards notice they are getting air attacked. Shaw orders to follow procedure, and they fire missiles. They hit the Blackbird!
Back in Portland, Synch, Charlotte and Leech move out of their hideout, having survived the Sentinel attack. Suddenly, a bright light surrounds them. Charlotte tries to identify herself as a civilian with a passport, but the attacker doesn’t care. Baron Zemo and his Thunderbolt army step forward. Zemo dares to wager that Charlotte and her friends have all the required papers faked, but it doesn’t matter to him. Leech wants to attack the Nazis, but Synch holds him back as he knows they are dangerous. Charlotte asks Zemo what he wants from them. Zemo applauds the directness, and explains that he wants both Magneto and Jubilee. In return, he’ll help Charlotte and her friends.
At the Dam, Magneto manages just in time to pull up a force field and rescue himself and the others. Magneto explains that the close call was his intention, as he knows that Shaw’s men will now search the wreck and it will take a couple of hours before they realize there aren’t any bodies inside. Shaw’s men have to believe that Magneto and the others are dead, so that Wolverine has a chance to get inside the building unnoticed. Magneto is aware that, if he would join Logan, they would surely be spotted and Wanda wouldn’t survive.
Meanwhile, Wolverine merges from the sewers, and climbs his way up inside the building. Logan does what he does best, and manages to sneak around to the room where Wanda is held. He quickly takes out the guards. Wanda wakes up, and asks Logan what he’s doing there. Wolverine promises he’ll be soon with her, but hesitates, as he hears a noise behind him.
Midnight strikes! Wolverine quickly snikts his claws open, and they start fighting. Logan knocks her down, and recognizes Midnight’s scent. Midnight defends that Logan’s sentences could be lying to him, but she doesn’t want to. She pulls off her mask, and reveals herself to be… Amiko! Amiko refuses to act mysterious any longer, and pulls out her sais, which she stabs into Logan’s back! He starts to bleed. Normally, Amiko admits, he would allow Logan some time to recover, but this time, her sais were poisoned.
Amiko gets closer to Logan, so that only they can hear her whisper to him. She calls him an idiot, as though she has tried to stop Logan, she didn’t want this meeting. She knows that Logan is a noble person and could have stayed out of this. Logan tries to say something, but Shaw and Betsy show up. Shaw congratulates Midnight on her victory, and realizes that, should Logan ever wake up, the chaos would be too big to restore. So, he activates the machine Wanda is held in, and her powers go berserk! She screams, like it is the beginning of the end!