Comic book writer Chris Claremont's Uncanny X-Men storyline "Days of Future Past" (1981) is the basis for director Matthew Vaughn's developing sequel to X-Men: First Class, wherein the concepts of time-travel and alternate realities will be introduced in an attempt to make sense of the disjointed X-Men continuity.
Days of Future Past will therefore be bridging the gaps between the original X-Men trilogy, First Class, X-Men Origins: Wolverine, and director James Mangold's (3:10 to Yuma) The Wolverine - an installment which, as it were, draws from Claremont's work on "Wolverine" Issues #1-4 from back in the early 1980s.
Hugh Jackman (who is reprising his iconic role in The Wolverine) has clarified that while Mangold's film does take place after the events in Origins, the film is being structured as a standalone picture - one with a distinct visual aesthetic to set it further apart from other X-Men movies - that focuses on Logan's plight. That sentiment gelled with previous comments from Mangold, who said the script is a character piece (with noir and foreign-language elements) that stands outside the archetypical superhero movie mold.
Fox has hired Mark Millar (writer of the Kick-Ass comic books and Marvel Civil War limited series (2006-07)) to serve as an architect overseeing in the construction of a cohesive Marvel/Fox cinematic universe. However, principal photography has already begun on The Wolverine, meaning that Millar won't have much (if any) significant creative input on the film. Hence, it's just as well that Mangold isn't making a conscious effort to further-develop any major narrative threads from the rest of the X-Men movie franchise.
The expectation has long been that Wolverine will take place prior to the events of the X-Men trilogy, with Logan (who has no memories of his past) on an adventure in Japan where he romances the daughter of a powerful family who is promised to someone else, setting him on a collision course with such dangerous figures as The Silver Samurai and Madame Viper. However, during an interview with Empire, Mangold revealed the film is set after the events of 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 [Wolverine]."
We know from set photos that Wolverine will also feature flashbacks to Logan's past (including, his experiences in Japan during WW II), as evidenced by an image of Jackman wielding bone claws published in the latest edition of Empire Magazine. Mangold's suggestion is that, by examining the character's history from a contemporary setting (one where the currently-defunct X-Men 4 would have taken place), it should allow for a deeper exploration of Logan's psychology and struggles with his regenerative abilities - since there won't be other major mutants or superheroes to distract from that task (as happened in Origins):
"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. 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."
Wolverine was long expected to take place prior to the X-Men trilogy, for reasons similar to those Mangold mentioned. Whether the setting resulted from changes that Mark Bomback (Live Free or Die Hard, Total Recall) made to the original script draft from Christopher McQuarrie (The Usual Suspects, Valkyrie) - or if the 'future setting' was planned from the very beginning - is unclear.
Days of Future Past, as mentioned above, aims to 'correct' the contradictions in cannon that have arisen between the five X-Men movies released to date, and The Wolverine won't obstruct that effort. If anything, the decision to have the latter set after The Last Stand should allow for a richer performance from Jackman, now that he can draw from three additional movies of character development (rather than having to revert to the mindset of an amnesiac Logan).
The Wolverine is directed by James Mangold off of Mark Bomback and Christopher McQuarrie’s screenplay. It stars Hugh Jackman, Svetlana Khodchenkova, Will Yun Lee, Brian Tee, Hiroyuki Sanada, and Rila Fukushima.
Look for The Wolverine when it hits theaters on July 26th, 2013. X-Men: Days of Future Past will arrive on July 18th, 2014.