Marvel Comics Wolverine: The End
Although Wolverine's ongoing story is still being told, he did get his own miniseries for Marvel's 'The End' event. It must be noted that 'The End' is not part of the canonical Marvel Universe, it is just a potential future.
In this series, purporting to be Wolverine's last adventure, Logan is an old man living in the Canadian wilderness. His only friend is an old man called George, who has been getting him groceries since he was a child. Logan knows that, despite his healing factor, he will die soon. He doubts his own sanity and his memories, including the Weapon X program. This doubt is exacerbated by the spirit of Professor X, who lives on (in diminished capacity) in Logan's mind.
One day, he decides to prove himself finally wrong or right. He travels to the ruined Howlett estate, where he finds the old grave of a young boy named James Howlett. Someone had left a book on it earlier that day. Paranoid, Logan decides to return the book to its library in rural Japan. When George tries to talk him out of it, Logan accuses him of being a Weapon X agent, but then apologizes, asking him to check a stack of magazines in his cabin, saying 'one of them ain't right. It ain't… me, if ya follow".
Logan goes to Japan. On the way over, he reads the book, called 'Lost Secrets of the Kamkuri', which is a factual account of an extinct evil Shinto sect of disputed reality. When he arrives at the library, he breaks up a Kamakuri ritual, asking are they working for Weapon X. The leader of the group declares his allegiance to the White Ghost, before being killed by a shadowy figure. Logan follows the figure up the mountain, where he is attacked and left for dead. The White Ghost says, "I could have killed you, old man. Any time in the last two hundred years, I could have killed you." Logan replies, "Then why didn't you?".
Back in Canada, George goes through the magazines. Among Popular Mechanics and Custom Bikes, he finds Wine Lover, to which he remarks, "you sly old fox". Based on a note in the magazine, George is able to access Logan's computer, to notify the authorities that Logan has gone to Japan and may need their help.
In Japan, Logan wakes up. He discovers that the White Ghost is none other than John Howlett, his brother, presumed dead during Logan's childhood. He is a mutant, with Logan's bone claws and healing factor, but also the power of intangibility (similar to Shadowcat). He used these as a spy. With this and his share of the Howlett fortune, he became rich. He became involved in the Weapon X program, and watched Logan all through his life. He promises to tell Logan everything as soon as he completes his scheme: to teleport an atomic weapon into the atmosphere over Las Vegas. With this act, the American economy will collapse, and mutants will ascend in the resulting chaos. Logan fights him, eventually pushing them both out a window. He lands below, accidentally impaled on Logan's claws… With his dying breath, he tells Logan he's sorry that he doesn't remember about Rose. John dies in Logan's arms, just as Japanese attack helicopters arrive with orders to destroy the compound and all its occupants, Logan included.