Wolverine, standing in front of some phone booths, hesitates on calling someone. Instead, his cell phone goes off and he picks it up. It’s Emma, wanting to know what Logan’s first move is going to be. Logan mocks that Emma tells him since she’s the mind reader. Emma mentions that Logan sounds angry. Logan doesn’t think that’s much of a surprise, since soldiers have been so much over him lately it isn’t funny anymore.
He jokes that SHIELD must be sweating bullets with him slipping in and out of the grind so much. Emma thinks so to. And, she adds, in light of recent events, she’s certain that Logan can understand SHIELD’s reason. Logan wants to know if Emma is going to try and stop him. Emma won’t, but she won’t help Logan either. But, since Logan is, Emma can tell him this: she doesn’t know where the person is Logan wanted her to find. Logan doesn’t like that. But Emma is certain that, if anyone can find the guy, it’s Logan, and she wishes him good luck.
Logan hangs up the phone and, while holding a package, he takes off, heading downtown. A few moments later, he hits into a bar called Shinjuku. An operative agent reports back to his colonel about Logan’s whereabouts. The colonel fears that his soldier has probably been spotted by Wolverine and wants him to pull back. The soldier, confident that won’t be the case, as there are over twelve million people in this city, wants to continue the mission. The colonel doesn’t think so and orders the agent to do as ordered. He wants to give Logan enough time to feel relatively secure and then send someone else in to find out what he’s up to. He knows that the last thing the soldier wants to do is confront Wolverine in a close-quarters situation.
Wolverine himself heads deeper inside the bar, where two goons are guarding a locked door. They refuse to let Logan pass, but he’s too impatient and in return knocks them both out! After doing that, he makes it to the bathrooms. But the battle soon gets spotted. The goons’ boss shows up and knocks on Logan’s bathroom door, reminding him that he is in an exclusive club and has to wear a suit. Wolverine, tossing on his X-Men uniform, jokes that he’s putting his suit on right now.
Once his uniform is on, Logan quickly snikts his claws through the door, hitting the boss through his stomach! He begs for mercy, which Logan promises to grant, but only for one thing in return.
The colonel asks his soldier what the situation is. The agent doesn’t know. He tried entering the club, but security guards won’t let him pass claiming a private party is going on. The colonel informs and warns his other agents that their subject has gone underground.
Wolverine has dug a hole into the bathroom floor and is now in the subways. He slices a security lock apart and makes it to the train rails. Once a train passes, Logan jumps on it unnoticed.
A few minutes later, spies realize that Logan is getting near and alert all of their friends, who now operate from an office tower, a parking lot, the private party and the surrounding rooftops. Everyone is ready to bring Wolverine down, should it be needed. Their boss is glad to hear that and suspects that their guest should be arriving momentarily via an underground tunnel.
Logan jumps off the train and starts climbing up a wall. He uses the wires around it to help him move up, until he has reached the spot where he wanted to go. After counting until one hundred and fifteen, Logan stops countdown as he made it to a sewer hatch. Above the sewer, a car makes it nearby. Logan quickly snikts out his claws and slices them through the car, causing the chauffeur to lose control over his steer and hitting another car!
A SHIELD soldier warns Colonel Dugan that they’ve got a major problem, as it would seem that Wolverine has just attacked the prime minister of Japan’s convoy! Dugan is at least glad to finally know where Logan is. He orders someone to let the Japanese government know that they are aware of the situation and mobilizing agents immediately, wanting to see the Japanese this as SHIELD’s “official” statement. Unofficially, Dugan wants one of his soldiers to advise SHIELD’s Section Chef the following order: all SHIELD agents are to clear of the incident site until Dugan gives the word.
The SHIELD soldier is confused. Dugan doesn’t know why Wolverine attacked, but is certain Logan picked the perfect spot to do it. There’s no way to bring in air support and near-zero mobility. Dugan panics, fearing Wolverine is going to turn that tunnel he’s in into a meat-grinder. Dugan thinks it might still have a chance that this situation won’t go completely south on SHIELD, though. He explains that the prime minister recently acquired a new captain for his personal security cadre. A man that goes by the name of… the Silver Samurai!
At the tunnel, Wolverine starts attacking some criminal, dodging all of their bullets. Once they are all dead, the Samurai steps forward. Logan, holding his claws ready, mentions to the Samurai that he’s a hard man to find. The Samurai thinks that may be the case, but mocks that, as Logan might have forgotten, he’s also a hard man. The Samurai takes out his sword and tries to hit Logan, but fails, as Logan blocks it using his claws. While the two super-powered individuals battle, the prime minister’s chauffeur notices his chance and drives them into safety.
Dugan is reported about the turn of events. He’s glad that the minister is safe again, and orders his right-hand soldier to have his troops run escort, thinking it will be good some good public relations. And he also wants to be informed when Logan pops back up on the grid. The soldier promises he’ll do that and leaves. Dugan heads to the communication room, where he receives a phone call. He assumes the caller is aware of the situation and gets a confirmation. Dugan wants that the rest of them gets filled in about what’s going on, because he and the other Avengers are very curious to hear about it.
Emma can only tell them that the situation is not what it seems. Captain America thinks it seems like Wolverine has jumped the fence again and that, this time, he has gone after a Head of State. Emma, correcting Cap but not wanting to sound insulting, mentions again that the situation is not what it seems to be. Dugan is interested in knowing what the situation really is then and what Logan is doing, and why. He knows that the X-Men know Wolverine better than anyone, even better than Logan knows himself. Emma corrects that might have been the case once, but not anymore. She reveals that Logan has regained his memory!
Startled to hear that, Dugan wants to know if that’s truly the case. That Logan remembers all of his… real memories. Emma confirms.
While the communication between SHIELD and Emma gets hijacked by several other governmental offices, they all start destroying files, with some being related to the Weapon X Program. Even a building gets torched, and one man shoots himself!
All of the Avengers are surprised that Wolverine has his memory back. Dugan corrects Emma that Logan having his full memory back isn’t a good thing.