Kitty Pryde hovers above the courtyard of the Xavier Institute in her pajamas. The courtyard is filled with armed SHIELD agents. Kitty phases into one of the mansion’s living rooms where her roommate Rachel Grey AKA Marvel Girl is watching television. Kitty informs Rachel that the SHIELD agent that she likes is on duty again. Rachel tells Kitty that she touched his mind earlier and learned he had a girlfriend and baby. The two X-Women agree that most men are creeps.
Kitty asks why Rachel is still up and she explains that the Institute’s students are keyed up over the situation with Wolverine and that their dreams were keeping her awake. Kitty brings up that Hydra and the Hand have snagged Elektra and turned her as they did Wolverine. Rachel tells Kitty that the SHIELD agent said that this was the rationale behind the increased security detail at the Xavier Institute. Kitty reminds Rachel that it’s the President they’re after. Rachel says that she thinks that the President will be safe with all the super-heroes they’ve flown in to protect him. Kitty cynically suggests that maybe that means they’re the ones who should be worried. With that said, Shadowcat heads up to bed by phase-walking through the ceiling.
Once she is gone, Rachel tells an unseen party that he can turn visible again. It’s Wolverine who has been present and cloaked the entire time. Wolverine reminds Rachel of the deal: she does exactly what he says and he won’t activate the terra-former he stole from Reed Richards. If he did so, it would clear the surrounding area and kill all those within a given radius, including everyone at the Institute.
Wolverine drags Rachel by the neck and pulls her forcibly to the Cerebra chamber. As he goes, his Hydra programming echoes in his mind and commends him on his performance so far but chides him for feeling sorry for himself. He also notes that Rachel looks a lot like her mother.
Wolverine uses his Hydra implants to bypass Cerebra’s codes and re-calibrate the system to accept Rachel as a user. Wolverine tells Rachel that the plan is for her to kill the President telepathically using Cerebra. She tries to protest and Wolverine reminds her that half a million people will die if he sets off the terra-former.
In Washington, Captain America and Nick Fury are in the Oval Office with the President. A SHIELD agent reports that Hydra has snagged another superhuman, a 14-year-old from Iowa with invisibility powers. The President says there’re only six minutes left to the midnight deadline and feels assured that nothing will happen. Captain America disagrees and thinks that Wolverine is coming.
Rachel is now hooked into Cerebra but tries to remind Logan that he was once one of the good guys and that protecting the students at the Institute was his job, too. Wolverine tells her that she’s good but no Jean Grey and not to play games with him.
Meanwhile, Iron Man is flying over Washington, DC scanning for any signs of a threat to the President. He comes up with nothing.
As Rachel activates Cerebra, Wolverine’s dual consciousness is arguing over the young telepath. His Hydra programmed personality is ogling Rachel and once again comparing her to Jean. Wolverine’s true psyche protests and warns his “Hydra persona” not to touch her.
Rachel confirms that she has locked onto her target and Wolverine tells her to give him a nice, big brain hemorrhage. Wolverine’s Hydra conditioning continues to go on about Rachel and the pheromones she gives off when Wolverine’s around. Logan tries to silence the programming in his mind, which goes on to make lustful comments about Kitty and Storm.
This provides enough of a distraction for Rachel to act. Much to his surprise, the terra-former instantly disassembles in Wolverine’s hands. Wolverine wonders how she managed to take apart such a complex machine so quickly. Rachel explains that she used Cerebra to contact Reed Richards and telepathically gain the understanding necessary to disassemble the device without detonating it.
Rachel removes the Cerebra helmet as Logan unsheathes his claws. She lashes out with her telekinetic powers sending Wolverine crashing through the door to the Cerebra chamber. Rachel emerges from the chamber, the Phoenix symbol over her left eye glowing menacingly. She telepathically alerts the other X-Men to Wolverine’s presence.
At Hydra’s headquarters, Baron Von Strucker orders a technician to get Wolverine out of there. His wife, Elsbeth watches with apparent derision.
Wolverine is teleported away from Rachel to another floor where he is spotted by Northstar and a group of students. He continues to teleport throughout the Institute and Rachel tracks him telepathically by reading the reactions of those who encounter him. Wolverine goes to the hangar and fires up the Blackbird. He pilots it through the heart of the Institute, nearly colliding with Rachel, Cyclops and Emma Frost. The Blackbird tears through the roof of the mansion and flies into the neighboring woods.
The X-Men assemble and pursue Wolverine. Storm drops the temperature in the woods to make it less comfortable for Wolverine. Logan stops the Blackbird and flees on foot.
At Hydra’s base, Elsbeth wonders how many jaunts they have left to help in getting Wolverine out of there. Baron Strucker assures her that Logan will escape.
Wolverine’s dual psyches continue to war against each other as he is hunted by the X-Men. Northstar leads a group of flying students in the search, though only tenth grade and above are allowed to participate.
The X-Men, students and SHIELD agents fan out to scour the woods. Wolverine takes out two SHIELD agents and draws the attention of Emma Frost. Havok is the nearest to Wolverine and unleashes a plasma burst that destroys the tree Logan was hiding behind. Logan advances and slices through Havok’s mid-section with his claws. The Beast tackles Wolverine who manages to subdue him in a single move. Wolverine smells Rogue and Gambit advancing as well as others and teleports again.
Iron Man and Captain America arrive to join the hunt. Northstar notes to Kitty that it is as if they are hunting Magneto. He comments on how changed Wolverine is. Kitty reminds him that Logan has been brainwashed and to just stay cool about things because the students are looking to them to gauge how to react to all this.
As Kitty tries to reassure Jean-Paul, Wolverine lunges at her. She phases at the last moment and Wolverine passes through her and collides with Northstar. He slams Jean-Paul into a tree and pops his claws directly into Northstar’s chest.
Kitty hits Wolverine over the head with a thick branch. Cyclops then arrives and pummels Logan with a full-force optic blast. The X-Men advance and Wolverine uses his final “jump” to teleport away.
He is badly hurt and needs time to recover. He thinks to himself that he wished he had never tried to help that kid in Japan in the first place. He mumbles that he needs to get himself together. At that moment, Captain America slams his shield down on Logan’s head, driving him down into the mud.
Captain America calls for a SHIELD team get Wolverine secured and cleaned up. Falcon is present and gives Captain America “props” for taking Wolverine down. The casualty reports indicate that Wolverine killed eight more SHIELD agents and injured four more. Havok has serious wounds but will survive. Northstar was not so lucky. The X-Men gather around as paramedics arrive. Kitty says it’s no use, that Northstar is dead. She is horrified at what Wolverine has done.
At Hydra’s base, Elsbeth demands that her husband Wolfgang step down as leader of Hydra. She assures him that his contributions will be remembered and that Elektra will succeed where Wolverine failed. He bows before the Gorgon who is installed as the new leader of Hydra.
On the SHIELD helicarrier, Nick Fury and Captain America watch as medical teams monitor Wolverine and keep him sedated. Fury notes that they considered killing him, but that he might have valuable intel. Plus, it wasn’t fully his fault. Cap notes that Wolverine never seems to get a break. Fury notes that they’re in for a world of trouble now that Hydra is being led by the fanatics on the fringe. Cap wonders if SHIELD has a plan and Fury smiles as he looks down at Wolverine and notes that they have their “little killing machine” back.