In X-Men: The Last Stand, we saw that Wolverine kills Jean Grey and Scott Summers was killed. Later, In The Wolverine, Logan recovers from his past. However, in X-Men: Days of Future Past, Scott Summers and Jean Grey were there (who were killed in Last Stand). This movie is the sequel of X-Men Last Stand. If this is so, then why does X-Men: Days of Future Past show Jean and Scott alive? Where does the timeline of both movies lie exactly?
According to the Fox executives, the storyline in Days of Future Past has erased all of X-Men 3: The Last Stand's storyline from canon, as well as parts of X-Men Origins: Wolverine.
In-universe, everything that happened in the first X-Men trilogy occurred in the original timeline, where Mystique kills Trask in 1973. Once Wolverine is sent back and stops her, it changes the future, so none of those events have happened.
Out of universe, it looks like Fox is going to continue to acknowledge the events of X-Men, X2: X-Men United, and The Wolverine as happening in some form in the new timeline, as well as First Class (which happened earlier in the timeline). In this timeline, however, Jean doesn't kill Scott, and Wolverine doesn't kill Jean. (There appear to be a number of other slight differences, which I assume will become clearer over time.)
The next movie, X-Men: Apocalypse, takes place chronologically before X-Men, so we may also see some of those events happen in a slightly different way with the same result.
Days of Future Past shows two timelines at the same time. It's a sequel to Last Stand, at a point where everything has gone to hell. All the events that happen before the last ten minutes or so, happen in the original timeline where Last Stand happens.
After the past is changed (Trask is not killed, Mystique saves Nixon on international television), the original timeline is wiped out, and replaced with a timeline where everything did not go to hell. This is the new timeline, where the original trilogy did not happen as shown. Since mutants are no longer persecuted (as much), events did not happen the same way. Jean did not become the crazy Phoenix, and Fox did not write off Scott in favour of Wolverine.
YES, most parts of Days of Future Past makes it a canonical sequel to The Last Stand. Much of the first few X-Men films' (released) EVENTS (such as the events in the The Last Stand) are erased or altered by events in Days of Future Past, but not necessarily irrelevant or completely altered.
“The end of Days of Future Past in 1973 does change the timeline of the established film universe. But one of the things we posit in the film is the immutability of time. So what you see at the end is a future that has been shifted but not completely transformed. Our characters are back in the mansion, as we saw them in X1-3, with some obvious changes (like certain characters being alive). So the answer is yes and no. Yes it changes the timeline. No it doesn’t completely erase everything…” http://collider.com/x-men-days-of-future-past-ending-explained/
"I don’t know if you were born or were alive in 1973, but I was, and as far as I know, a stadium did not drop on the White House," Kinberg said, laughing. "All human history has changed after Days of Future Past, not just whether Jean or Scott lived or died. What that gives us, which is great fun, is we can also mess around with human history. We aren’t beholden to everything that happens in future X-Men movies being secret, because if you were to hold to the original X-Men movies, at the beginning of X-1, it’s really the first conversations about mutants in the world. But if in 1973 a stadium fell on the White House or in the 1980’s there was an apocalyptic event, conversations would have started much earlier."
The Following is the order of the Films in relation to event history canon. I have included what timline the films belong to too, using "A" and "B" generally. Some films are mentioned twice, because they feature multiple time periods, in which, some time periods are then true or unaltered in both timelines. (However, there is some inconsistency or continuity errors no matter how you slice it)
X-Men Apocalypse (Ancient Egyptian past same for both timelines)
X-Men: First Class (same for both timelines)
X-Men Origins: Wolverine (Flashbacks - Timeline A)
X-Men (Timeline A)
X-Men Origins: Wolverine (Wolverine leaves to find answers - Timeline A)
X2: X-Men United (Timeline A)
X-Men: The Last Stand (Timeline A)
The Wolverine (Timeline A)
X-Men: Days Of Future Past - The timeline is split and changed through conscience-time-traveling Wolverine. We see a new past being made AND a new future being made by the end of the film, but pre-conscience-time-traveling-Wolverine parts of the past in the film, would also be the same in both timelines.
X-Men: Apocalypse (1983 - Timeline B)
X-Men: Dark Phoenix (Upcoming Feature - Timeline B, but may play with space-time)
Note: One probable reason most of timeline A was erased after Days of Future Past, was to bring in a younger cast with retro-setting to get a younger demographic audience on board with the franchise. It was one way to revitalize it.
Time travel - Many of the X-Men's stories delve into time travel either in the sense of the team traveling through time on a mission, villains traveling through time to alter history, or certain characters traveling from the past or future in order to join the present team. Story arcs and spin-offs that are notable for using this plot device include Days of Future Past, Messiah Complex, All-New X-Men, Messiah War, and Battle of the Atom. Characters who are related to time travel include: Apocalypse, Bishop, Cable, Old Man Logan, Prestige, Hope Summers, Tempus, and Stryfe...
Reflecting social issues The conflict between mutants and normal humans is often compared to real-world conflicts experienced by minority groups in America such as African Americans, Jews, various religious (or "non-religious") groups such as Muslims and Atheists, Communists, the LGBT community, the transgender community, etc. It has been remarked that attitudes towards mutants do not make sense in the context of the Marvel Universe, since non-mutants with similar powers are rarely regarded with fear; X-Men editor Ann Nocenti remarked that "I think that's literary, really - because there is no difference between Colossus and the Torch. If a guy comes into my office in flames, or a guy comes into my office and turns to steel, I'm going to have the same reaction. It doesn't really matter that I know their origins. [...] as a book, The X-Men has always represented something different - their powers arrive at puberty, making them analogous to the changes you go through at adolescence - whether they're special, or out of control, or setting you apart - the misfit identity theme." Also on an individual level, a number of X-Men serve a metaphorical function as their powers illustrate points about the nature of the outsider. https://en.wikipedia.org/wiki/X-Men
However, from an ongoing story perspective, one can argue it was a good move being true to X-Men in the comics, because X-Men in the comics (and just being apart of Marvel's MCU), provides multiple universe or timelines already as a way to examine who someone could be and clearly goes with X-Men's identity diversity & social justice themes. By the end of The Last Stand, many comic fans were mad because clearly Jean Grey was possessed by another entity, Dark Phoenix, but the films did not explore it, making it clear the X-Men didn't know what it was, resulting in many characters' untimely deaths. So using Wolverine in particular, someone who came and upset the balance of Jean's life and in which he could not save her or Scott, paved the way for a redemption story that may finally be realized in the next main X-Men film, since the film is revisting that entity. Wolverine is then perhaps acting as a course-corrector to the time line, pending what the future X-Men films are going to look like, which may be on the fritz now that Disney is in the process of buying 21st Century Fox.
I have read conflicting statements about "when" (in what timeline) this is set. Some believe it is the new 2029 further-future that Logan returned to at the end of Days of Future Past and others believe it is in yet another timeline's future. In either case, it's clear that this "future" Wolverine counterpart has experienced many of the same things from the previous two timelines Wolverine counterparts and that the Western genre elements presented through a rugged realism landscape provide a realistic look onto the concept of myth and legacy by looking back onto the other films' events.
Other X-Men Films/TV Series - Where do they belong?
Landgraf stated, in January 2016, that the series would be set in a universe parallel to the X-Men films where "the US government is in the early days of being aware that something called mutants exist but the public is not".
The producers hoped that audiences would watch the show because of its character-focus and the talents of Hawley and the cast, rather than to "see a Marvel franchise show."Donner also noted that having Hawley focus on Haller's perspective of reality rather than connections to the X-Men films allowed the series to avoid the convoluted continuity of the films, "because we play with so many different timelines, and we rebooted and not really rebooted and all that" throughout the films. Therefore, "the cinematic universe will not worry about Legion. They will not worry about these TV worlds at all. https://en.wikipedia.org/wiki/Legion_(TV_series)
“It’s not in the continuity of those films in the sense that the current X-Men films take place in a universe where everybody on planet earth is aware of the existence of mutants. Legion takes place in a parallel universe if you will where the government is aware mutants exist but the public is not. I wouldn’t see characters moving back and forth because they really are parallel universes.”http://www.slashfilm.com/x-men-tv-series-legion/
"What's nice is Deadpool exists in his own universe. He's part of the larger X-Men universe, but in a way he isn't. He interacts with that world but he is in the present. We don't deal with the '60s or the '70s or the future. It's here and now. More than anything, I think he's going to have his fun with what they do in the other franchise. But fortunately, we don't have to play by those same rules. Deadpool is a movie that did break all the rules.http://comicbook.com/marvel/2017/01/26/deadpool-writers-explain-how-the-movie-fits-into-the-x-men-timel/
- The Gifted:
The Gifted is an American television series created for Fox by Matt Nix, based on Marvel Comics' X-Men properties. It is connected to the X-Men film series, set in an alternate timelinewhere the X-Men have disappeared. The show is produced by 20th Century Fox Television in association with Marvel Television, with Nix serving as showrunner. https://en.wikipedia.org/wiki/The_Gifted_(TV_series)
Legion (no X-Men organization), Deadpool (fourth wall breaker, X-Factor leanings), The Gifted (X-Men mysteriously disappeared and features many secondary X-Men characters), are set in their own parallel universes respectively.
New Mutants (planned horror trilogy) - Is said to have some kind of connection to the main X-Men films, but was also discribed as though it may exist in it's own courner of the over all franchise.
X-23 Logan Sequel/spin off (pending Disney's plans)