The film opens with a flashback to 1945 Nagasaki, where Logan (Hugh Jackman) is held prisoner by the Japanese.
As the bomb detonates, Logan protects one kind officer, Shingen Yashida, from the radiation blast - his mutant powers allowing him to recover almost instantly from the fireball.
Years later, Logan is living alone in the woods, haunted by the death of Jean Grey.
A swordswoman called Yukio (Rila Fukushima) tracks him down and asks him to go to Japan to meet with the old and frail Shingen.
Reluctantly, Logan agrees and he is shocked to find Shingen (Horiyuki Sanada) on his deathbed. Soon after, Shingen dies and the Yazuka attempts to kidnap beloved granddaughter Mariko (Tao Okamoto), who is poised to take over the family dynasty.