The film carries on from the end of X3, with Wolverine “in hiding” after killing Jean Grey, and haunted by her ghost. After being “hunted” by an assassin, he goes with her, in order to “say goodbye” to someone he saved in his past. When he is met by the man, he is given the chance to have his immortality taken away and live as a normal human, something which he think will be a curse to whomever has it. He then gets involved in a conspiracy involving the mans granddaughter, who is being hunted by what we assume in the Yakusa. Logan protect the girl, taking her somewhere she wont be found, and eventually formed a connection with her, at the same time he realises that his power is being suppressed, and that he can actually be hurt. When the girl is finally kidnapped, Wolverine realises how his powers are being suppressed, teams up with the assassin from earlier, and goes to save the girl, who is being held by her own grandfather, who using a new suit, tries to take away Wolverines powers forever. Wolverine overcomes it, and goes back to being what he was before, a soldier.
The film works in two parts. It works as a way for Wolverine to get over killing Jean Grey, who appears to him as a ghost. It is his guilt of having killed her, and the fact that he may never join her in the after life, but it also works as death itself, often calling for him to join her. The film has Wolverine pining over her the whole film, but in the end, he realises that he wasn’t at fault, and that when he’s ready he will join her, essentially working as a way for Wolverine to get over her death, and pass the mourning he has for her
The film also works as a mortality tale, something Wolverine sees as both a blessing and a curse. His healing factor has given him a sense of immortality, and allows him to fight without fear, but it also has shows him how quickly life passes him by, with him seeing loved ones dying. Most of the characters in the film at one point have to face their mortality, Yashida, isn’t ready to die, and wants to live forever, maybe being scared of death. Mariko has a hit out on her life, and has to deal with her life being in mortal danger. Logan has to deal with actually being mortal, and his wounds not healing, as well as the ghost of his death lover haunting him, asking for him to die so they can be together. It is something that Logan hasn’t had to think about, dying, he usually is concerned with others dying, but when confronted by his own death, he looks at it head on, and knows that it isn’t his time. Yukio like Logan has to deal with others dying, with her power being seeing peoples deaths.
Wolverine is a soldier, or in the films case a Samurai, someone who works for the good of someone else, he isn’t a man who necessarily wants to lead, but someone who can follow, and will do everything in order to protect those he cares about.