In an old Yashida clan cemetery in Japan, Logan meditates at Mariko Yashida's grave. Gambit, Jubilee, and Yukio worry about Logan because he has been meditating for days. Logan thinks in his mind, he is torn between two lovers, Mariko and SilverFox. Wolverine suddenly lunges out with his claws, frightening Jubilee. Logan says he's fighting the beast inside that wants lash out at the pain and agony festering inside.

In New York City, Sabretooth is in the audience at a wrestling match. Shiva shows up to kill him, punching Sabretooth into the ring. The crowd think its part of the show.

In the subway, on the A train, John Wraith is approached by some hoodlums that bother him, but a Nazi gang boards the train, threatening Wraith and the hoodlums. Wraith threatens to kill the leader of the Nazi gang with a very lethal gun, the Nazi gang leaves at the next exit. The hoodlums turn to thank Wraith, but Wraith disappeared.

In Tokyo at Matsuo's penthouse, Matsuo Tsurayaba practices killing Wolverine with a new prosthetic hand that the fingers would turn into five blades of laminated steel, capable of slicing through flesh with ease. Hand ninjas tell Matsuo that Tokyo is not a safe for him, since Wolverine is in a crazed state of mind and might try to kill Matsuo, they tell him to leave for their remote island fortress, but Matsuo refuses to leave.

Yashida clan cemetery, Sunfire warns Logan that the Japanese government are not going to tolerate any type of revenge. Logan has a flashback of Berlin, Germany, Sabretooth, Maverick, and Wolverine were on a secret mission. John Wraith pulls up in a jeep, stays behind and fights the enemy, so the Sabretooth, Maverick, and Wolverine could safely get away.

In New York city, Sabretooth manages to pull off Shiva's head, but Shiva fire an electronic pulse that triggered Sabretooth's memory, where Sabretooth beats a little Logan for seeing Silver Fox. John Wraith appears, which pulls Sabretooth out from his flashback. Wraith uses an explosive device and destroys Shiva. Sabretooth and wraith escape.

In Tokyo, Jubilee and Gambit and Logan travel through the city to the airport in a limo that Sunfire had obtained for them. Logan refused to close the sunroof to the limo, allowing it to rain on him. Logan suddenly catches a scent, and leaps out of the limo through the sunroof.

In Matsuo's penthouse, Wolverine follows the scent to Matsuo. Hand ninjas attack Wolverine, but Wolverine easily kills them. Matsuo tells Wolverine that he is ready this time and unleashes his blades on his hand. Wolverine cuts off Matsuo's prosthetic hand. Matsuo believes Wolverine is going to kill him, but Wolverine explains that he is going to make him pay for a long time, each time Wolverine returns to Japan, Wolverine is going to cut off a new part. Wolverine cuts off Matsuo's nose and leaves, Matsuo falls to the ground.