In the Shinjuku District, Cyborg ninjas of the Hand trap the Noodle Vendor in an alley. Logan walks in to the alley and watch as the Noodle Vendor barley survives the attack. The Noodle Vendor tells Logan that he knows that he wants information from him and ask why Logan didn't help him. Logan tells him because he needed his rest for the real fight. Suddenly 8 Cyborg Hand ninjas attack them, Logan quickly cuts 7 of the ninjas to pieces, leaving the Noodle Vendor to kill one of them.

Akatora's Island in the middle of Tokyo Bay, Akatora, Emi and Sumi finally brainwash Amiko completley, making her think that Logan killed her mother. Akatora gives Amiko a small blade that had been coated in deadly blow fish toxin to kill Logan with, but tells her to bide her time, learn how to use the blade.

Halfway across the Tokyo Bay, Wolverine, Pale Flower, Yohei, and a reluctant Noodle Vendor arrive near Akatora's island. Wolverine jumps into the water to swim the rest of the way. On the Island, Akatora and his men prepare to film a scene, when Wolverine rises out of the water. Akator'a men attack with their cybernetic implants. Wolverine stabs two men in the chest, Wolverine claws get stuck in their chest, so he walks over to the third guy and kicks his cyborg head off. Akatora still on shore tells his Hand ninjas to attack Wolverine. Pale Flower and Noodle Vendor show up and fire machin guns into the ninjas. Akatora fires an uzi at Wolverine, who sheild himself with the cyborg bodies of his men. Akatora charges at Wolverine with a sword, and stabs it into his shoulder. Wolverine unleashes his claws and slashes Akatora across his face. Wolverine threatens Akatora with the Honor sword, if he doesn’t release Amiko. Pale Flower, Yohei and the Noodle vendor come out of Akatora's palace with Yukio and Amiko. Akatora reveals that Amiko will die because one of Wolverine's three friends was a secret agent of the Hand. Wolverine quickly throws the honor sword into the gut of Yohei. Pale Flower ask who Wolverine knew that Yohei was the traitor. Wolverine explains that Yohei was to skilled to be a Yakuza and he smelled like clove oil and blowfish toxin. Pale Flower realizes that Akatora had disappeared. Wolverine tells Yukio and Amiko that he has to go on a mission, but he will return to visit them soon. Amiko tells Wolverine that she could wait because she has a lot to learn while he is gone.