- Wolverine (Logan) (Main story and flashback)
- Yashida Zaibatsu (Only appearance)
- Keniuchio Harada (Only appearance; dies)
- Yashida Zaibatsu
- Noburo Mori (Only appearance)
- Yakuza (Only appearance)
- Jean Grey (Dream)
- Storm (Ororo Munroe) (Photo)
- Shizu (Only appearance)
- Saki (Only appearance)
- Mieko (Only appearance)
- Hitoshi (Only appearance)
- Trask Industries (First appearance) (Appears on a computer screen, TV, or hologram only)
- Magneto (Erik Lehnsherr) (Cameo)
- Professor X (Charles Xavier / "P. Xavier") (Cameo)
Races and Species:
- Earth-10005 (Main story and flashback)
- Earth (Main story and flashback)
- Japan (Only appearance) (Main story and flashback)
- Canada (Last appearance)
- Earth (Main story and flashback)
- World War II (Main story and flashback)
- Atomic Bombings of Hiroshima and Nagasaki (Main story and flashback)
In 1945, a POW camp near the city of Nagasaki, Japan is being evacuated after being informed of an atomic bombing coming their way. A young soldier named Yashida notices a man named Logan in a chained up well watching the commotion and attempts to get him out, but the prisoner refuses and advises Yashida to get away. As the bomb hits Nagasaki, Yashida and several soldiers try to commit honorable suicide, but Yashida is stopped at the last minute by Logan, who rushes the young soldier to the well and shields him while he takes the full force of the nuclear blast. Afterwards, Yashida witnesses Logan's regenerative powers in work, as it heals all of Logan's burns in a matter of seconds. The two climb out where Yashida is horrified by the sight of the destroyed Nagasaki.
Back in the present, Logan is now living as a hermit in Yukon after the events of Alcatraz Island and Jean Grey's death. Logan suffers nightmares and hallucinations of Jean after he was forced to kill her. He has also refused to go by his nickname "Wolverine" any longer. Later, Logan confronts several hunters for using illegal poisons to make a bear go berserk and kill other hunters. Logan is unable to thanks to the intervention of a Japanese woman named Yukio, who has the ability to see people's deaths.
Yukio brings Logan to Tokyo where Logan is to meet the elderly and dying Yashida, who has become a very wealthy millionaire thanks to his various companies. At Yashida's estate, Logan meets the old man, who muses that he has not aged a bit while Yashida is old and on his deathbed. While Logan simply wants to say goodbye in respect, Yashida reveals his true intentions: he wants Logan to transfer his immortality to him, allowing Logan to live a normal life while Yashida can live forever. Logan refuses, knowing full well the tragedies and consequences immortality can bring to one. With his last wish denied, Yashida instead begs Logan to keep watch on his granddaughter, Mariko, heir to his wealth and the target for many criminals for his wealth.
Logan is hesitant until Yashida seemingly dies as Mariko grieves. Yukio is saddened due to the fact that she was unable to predict Yashida's death.
- Hugh Jackman as Wolverine / Logan
- Hiroyuki Sanada as Shingen Yashida
- Tao Okamoto as Mariko Yashida
- Rila Fukushima as Yukio
- Famke Janssen as Jean Grey
- Will Yun Lee as Harada
- Svetlana Khodchenkova as Viper / Dr. Green
- Haruhiko Yamanouchi as Yashida
- Ken Yamamura portrays Yashida as a young man.
- Brian Tee as Noburo Mori
Additionally, Qyoko Kudo portrays Aya. Yaeko Kimura and Ryuta Kimura appear as Mieko and Hitoshi, respectively. Keiko Matsumoto and Kimi portray Shizu and Saki, respectively. Ian McKellen and Patrick Stewart make uncredited appearances as Erik Lehnsherr and Charles Xavier in the mid-credits scene.
- The film is not, as was previously believed, a prequel in the same vein as X-Men Origins: Wolverine and X-Men: First Class. Rather, events of the film take place after the events of X-Men: The Last Stand. Director Mangold said "Where this film sits in the universe of the films is after them all. Jean Grey is gone, most of the X-Men are disbanded or gone, so there's a tremendous sense of isolation for him."
- In an alternate ending, Yukio gives Logan an "interesting" gift on the plane before departure. The contents are a costume similar to his Earth-616 counterpart.
- Yukio's premonition of Logan's death in this film foreshadows his demise in Logan.