It turns out James Mangold's currently shooting "The Wolverine" is not going to be a prequel after all.
Talking with Empire, Mangold confirmed that while the project is based on the 80's-set Frank Miller-penned Japanese storyline, the events in this film definitely take place AFTER those in "X-Men: The Last Stand."
"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," says Mangold. "That’s something that for me was very important, that I land in a very specific place in his timeline. I wanted to be able to tell the story without the burden of handing it off to a film that already exists and having to conform to it."
Part of the reason is that it allows Mangold to explore some big themes: "The ideas of immortality reign very heavily in this story and the burden of immortality weighs heavily on Logan. For me that’s such an interesting part of Logan’s character that is nearly impossible to explore if you have a kind of league or team movie."
Despite this, there's been photos of Wolverine in a WW2 Japanese POW camp, and the article includes shots of Logan with his pre-adamantium bone claws. Throw in rumours of Famke Janssen's cameo and it seems fairly certain the film will feature flashbacks. Mangold calls the overall film a 'Japanese noir with tentpole action'.