Tokyo, officially Tokyo Metropolis, is one of the 47 prefectures of Japan. It is the capital of Japan and the most populous metropolitan area in the world.
During a mission at Alkali Lake, Wolverine encounters Lady Deathstrike. She knocks out Storm and locks her in a chest while she battles Wolverine in the eye of a hurricane - created by Storm in her panic. After Wolverine defeats her, Deathstrike escapes with HYDRA, the remaining Sentinels, and the Mastermold. Wolverine tells Storm he is going to follow because Deathstrike is a key to his past, however small. He promises to return as he attaches himself to Deathstrike's helicopter, which is en route to Tokyo, while Iceman, Storm, Colossus, and Nightcrawler return to the X-Mansion.
In Tokyo, Logan infiltrates HYDRA's main base and interrupts a conversation between Deathstrike and Silver Samurai, the latter telling the former not to feel dishonored by Stryker's method of controlling her. As he interrupts their discussion, the Silver Samurai flees, leaving Logan to fight Deathstrike. As they battle each other, he emerges victorious when she is crushed under a pile of rubble.
Logan then follows Silver Samurai to his base. He tells him that he is a mutant, and if he can defeat him in combat, he will tell him how to defeat the Sentinels through the Mastermold. The Silver Samurai's power is the ability to charge his sword with energy, letting it slice through nearly anything and channeling energy blasts through it. After defeating the Samurai in combat, Logan gains the information and informs the X-Men how to defeat Mastermold.
After Logan gets into a fight with some men at a bar in Canada, Yukio tracks his whereabouts and takes him to Japan to see the man he saved from the Nagasaki bombing in 1945, Yashida, now the head of the Yashida Corporation.
Logan meets Yashida at his home in Tokyo, who wants to return the favor by taking his immortality away from him and giving it to himself, who is dying of cancer. After Logan refuses, he meets his son Shingen Yashida and his granddaughter Mariko Yashida - whom he saves the life of following a suicide attempt.
The next morning, he attends the funeral of Yashida, where he saves Mariko from Yakuza assassins with the help of Kenuichio Harada. Wolverine gets shot multiple times and finds he is not healing as quickly as before.
After getting Mariko to safety, Wolverine follows her onto a bullet train, where he encounters more Yakuza assassins and kills them before they hide in a local motel. He stands guard in the rain while Mariko sleeps, and soon passes out from his injuries after having a hallucination of Jean. He awakens to find Mariko getting the motel owner's grandson, a veterinarian, to stitch him up.
After Mariko's kidnapping in Nagasaki, Wolverine and Yukio arrive at the Yashida home in Tokyo, where he finds the parasite on his heart. He starts to extract it when Shingen enters, with Yukio defending Wolverine. He dies in the process, but has his healing ability restored and revives, eventually killing Shingen. Yukio and Wolverine then follow Harada and Viper to the Yashida Research Center in northern Japan to find Mariko.