Despite being based on the classic Wolverine in Japan storyline that itself was a prequel to Wolverine’s time with the X-Men, the upcoming movie isn’t another prequel. I think that, aside form the awesome opening credits, everyone can agree that X-Men Origins: Wolverine was a steaming pile, so even if this retconned that; I don’t think we’d need another prequel. It’s time to move past Ratner pissing on the franchise with X3, and it looks like they finally are with The Wolverine and Days of Future Past.
Empire magazine spoke to the director, who confirmed the movie is set after the movie trilogy:
“Where this film sits in the universe of the films is after them all,” reveals Mangold. “Jean Grey is gone, most of the X-Men are disbanded or gone, so there’s a tremendous sense of isolation for him.”
Now those Jean Grey cameo rumors are starting to make more sense. There will be flashbacks in the movie to Logan’s time in WWII as they have released a shot to Empire of Logan with his bone claws.