Wolverine has been dropped into the Dam and wakes up, freaked out! Realizing the mess he is in, Logan recalls Amiko stabbing him with her poisonous sais. Logan grabs on an edge before falling down the waterfall. He snikts his claws open and tries to use them to help him up, but the water is too strong and Logan has the hardest time to safe himself. Suddenly, an arm grabs him, and pulls him up. It’s Amiko!
Amiko jokes that Logan is heavier than he looks. Logan wants to know why Amiko rescues him, as she was just trying to kill him. Or does she want to try it again? Amiko denies that, as it truly is her plan to rescue Logan. She knew that his healing factor could handle her poison. Amiko is surprised to learn that Amiko does love him. Amiko doesn’t respond, but thinks to the matter at hand: Shinobi Shaw’s deadly machine must be destroyed.
Meanwhile, Jubilee is getting impatient, as they haven’t heard from Logan for awhile. Magneto isn’t listening to her and he apologizes for it, but his thoughts were with his daughter. Magneto decides to go in. Jubilee tries to hold Magneto back and reminds him of the deal they had. Magneto promises to keep it but, if Logan failed to rescue Wanda, the least he can do is try it by himself. Magneto knows that Shaw and his goons are expecting him, but he doesn’t have a choice: Wanda is his child and the only thing he has left to be proud of. Jubilee understands, but wants to go with him.
Inside the Dam, Amiko leads Wolverine passed the guards as fast as she can. Logan asks her to wait, as he’s got so many things to ask her, but she suggests they do that another time. They duck, as Zemo and his Thunderbolts arrive in helicopters. Logan is surprised to find Zemo here, as he thought he was a thug of the Sentinels. Zemo goes inside the building, where Shaw is waiting for him. He informs the guards that he knows that Shaw loves defeated X-Men, so Zemo hunted the two last remaining ones down and arrested them. The guards climb aboard the helicopter, where they find Leech and Synch unconscious, with power dampening collars on!
They order them to wake up and move along. Wolverine has seen enough, and jumps to action and starts fighting the guards. He quickly takes them out, and uses one of his claws to release Synch and Leech from the collars. Amiko warns that they haven’t got any more time left, which is fine by Logan and tells her to lead away.
Somewhere else in the huge complex, Zemo greets both Shaw and Betsy. They tell Zemo he’s just in time, but he doesn’t know for what. Shaw jokes that the Sentinel High Council are wondering the same thing. Zemo hates being commanded by those robots. Shaw suggests that they better start with their plan then. But then, everything around them starts to shake.
It’s Magneto! He warns them that, if they release Wanda now, he’ll grant them a quick death, but otherwise their deaths will be slow and painful. Magneto turns his head around, and notices a screaming Wanda trapped inside Shaw’s machine. He gets furious, and shouts at Shaw that he’ll send him to hell!
He starts fighting and Betsy begins to panic. Shaw tells her to hold up for a few more minutes, as their computerized defense could be starting up any second now. Suddenly, Magneto screams! Shaw explains that he expected Magneto to drop in some day, so he installed some magnetic generators in all of the walls of the entire complex, and they create a force field on the same wave as Magneto’s mutant energies. And the best part is that Magneto will remain trapped for as long as he’s using his powers. And if he doesn’t use them, Magneto will still be vulnerable to Shaw’s strength.
Jubilee has jumped inside one of the soldier’s battle suits, and snuck past the combatants in the hope to shut down the machine. But Betsy realizes something’s wrong, and strikes in Jubilee’s back with her psychic knife! Betsy recognizes her former teammate, but does nothing but smile in an evil way. Shaw orders Betsy not to waste any more time, and to just kill Jubilee. Zemo agrees and laughs, as he always likes it when he can see an X-Man get killed.
Suddenly, Zemo gets struck by… a psychic knife?! He falls down, and Synch is revealed as the culprit. He has synched Betsy’s powers and just used them on Zemo instead. Betsy smiles, as she knows that Everett might copy her powers, but he hasn’t the skills to use them. Leech shows up, and touches Betsy’s arm, using his powers to shut down hers. Jubilee finishes the battle by throwing some fireworks at Betsy, knocking her out as a payback for betraying them.
Shaw shouts at the X-Men that they won’t leave this place alive. Wolverine and Amiko arrive and jump from the air vents down, not agreeing with Shaw. Logan jokes that he likes the idea of the good guys winning for a change. Amiko tells Logan he can have Betsy, as she’s already getting up after Jubilee’s attack. That’s fine by Wolverine, and he lands before Betsy. She confesses to Logan that she isn’t the shy girl any more that once fought as his side, and that she’s now in a body of a fully trained ninja and confident she can now handle Logan. He smiles, and knocks Betsy out with one single punch!
Logan moves towards Wanda, planning to set her free. Wanda notices Shaw sneaking up on Logan, and warns him. Shaw activates his powers and wants to strike Logan with them, but Amiko jumps between them, and gets hit instead! Shaw finds Amiko’s sacrifice a bit awkward and feel sorry, as she could have been his queen, but for the rest doesn’t care much if Midnight dies before her time. Wolverine notices that this is the second time Amiko saved his life today, and won’t let her sacrifice be in vain. He slices the machine’s control panel in pieces, and Wanda is released. Logan safely catches her in his arms.
Shaw shouts at Logan, calling him and his friends idiots, as he could have ended the tyranny of the Sentinels! Logan mocks that he prefers the Sentinels over Shaw any day. Suddenly, Shaw gets struck by a magnetic attack! It’s Magneto! Amiko has disrupted Shaw’s magnetic force field, so now he’s free again and can help out in the battle. Wanda is confused, and asks Logan if she’s really seeing her father. Logan confirms. With little breath left, Wanda asks Logan to tell her dad that he should never give up.
With the last strength she has, Wanda uses her Hex powers to fully destroy Shinobi’s machine. The entire Dam starts to break apart, and Logan thinks it’s best they leave. He grabs Amiko, who’s still alive. Logan doesn’t know who she really is, but won’t leave her behind. Shaw manages to open teleportation portals and escapes through them. Magneto asks Logan to take Wanda as well, as he wants to go after Shaw first.
Magneto finds Shaw still inside the Dam, and wants to make him pay for what he did to Wanda. Shaw defends that Magneto shouldn’t talk to him like that, as Magneto is the most hated and wanted man on the planet, and killing him won’t make people forgive his sins. Shinobi lets Magneto attack him, thinking that, without using his powers, he’s invulnerable. Magneto calls Shaw a fool, as even Shaw’s body is being kept together by electromagnetic forces, which Magnus controls. Magneto uses these skills to rip Shaw’s body apart and kills the man! But then, destiny strikes, and a heavy brick fall on Magneto’s body, and he collapses. He asks for Wanda.
Wolverine and the others find Zemo’s helicopters. Jubilee thinks they are perfect to use for their escape, and uses her powers to take out Zemo’s Thunderbolts. Leech has brought Betsy like Logan asked, but doesn’t understand why they have to take her. Logan remembers that Betsy used to be one of them, and won’t be left behind. Everyone steps inside the helicopter, and Wanda asks where her father is. Logan promises to go find him. Jubilee doesn’t understand why Logan made that promises, but he shouts that he has to do it, and orders the others to leave, now!
Logan goes back inside the Dam, and soon finds Magneto. He moves the brick, but the damage is bad. Magneto calls Logan a fool for coming back for him, but Logan shouts he didn’t. He did it all for Wanda. Suddenly, the Dam breaks apart and the untold gallons of water slide inside, trapping both Wolverine and Magneto.
The others notice the Dam breaking, and fear that Logan and Magneto are goners. However, Magneto has gathered all the strength he had left to create a magnetic force field around them, and transported him and Logan safely outside. But, Magneto is in a great deal of pain and can hardly keep himself together. Jubilee opens the helicopter’s door, and helps both men inside.
A few days later, everyone takes some time off to recover in Emma’s mansion. Magneto is stuck in a wheelchair and visits his daughter. He explains that his legs are crippled and that he will never walk again. But still, Magneto feels like a reborn man. He remembers that there were so many things he wanted to share with Wanda and her lost brother. Magneto admits that he never told them how proud he was of them and at the great choices in their lives they made. He feels sorry for not telling much.
Wanda tells her dad that he shouldn’t be stuck in the past. Magneto was who he was. She knows that, sometimes, you can start over and make a difference. She knows Magneto can do it. For her. Wanda touches Magneto’s face, and dies.
At the same time, Amiko meets up with a meditating Wolverine in the biosphere. Logan knows he’ll never forget Amiko’s scent. He wants to know if Amiko has come to tell her why she wanted him to believe her dead for all those years. Amiko realizes that Logan has earned to know the truth. Amiko explains that, sometimes as a kid, she was the victim of Logan’s enemies. Logan knows that, and admits that was the sole reason why he asked the Silver Samurai to protect her. Amiko understands but, a few years after that, the Samurai became emperor, and a danger as well. He thought it was safer that everyone believed Amiko to be dead. Everyone… including Logan.
Logan admits that the plan worked, as he was devastated when he heard about it. He wants to know how Amiko got stranded here. Amiko explains that she got tutored from the best warriors from the empire and they only knew her as Midnight. She wanted to become as good as Logan. And one day, the Samurai heard about Shaw and his machines. He told her to infiltrate in Shaw’s army and destroy them from within. She apologizes for lying. Logan admits that when he heard that Amiko was dead, something also died within him. And now, he’s just glad to have her back.
Emma, Synch and Leech are with Emma, and ask her about Betsy’s situation. Emma has discovered that Betsy has been hit hard. She has also spoken to her brother, Brian, and he’ll take her back to England until Betsy’s back to her former self. Wolverine asks Jubilee if she needs any more people in her rebel group. If so, he knows the perfect candidate: Amiko. Amiko explains that she has fulfilled her duties to the Japanese Empire, and would love to help out in the battle against the Sentinels. Logan mentions that Amiko isn’t a mutant, which might be handy.
Magneto enters as well, and explains that he wants to stay as well – if the group wants to have him. He explains that is Wanda’s final wish. Emma smiles, joking that miracles still happen. Logan welcomes Magnus in the group and wants him to remember that he volunteered by himself, because Logan is full aware that they’ll have a busy time coming!