The timeline of the FOX X-Men universe is one of the most muddled in existence: in certain movies, characters are too young or shouldn't have been born yet; some characters are duplicated; and backstories don't seem to line up. I think I can offer an explanation: time travel and altering history in X-Men doesn't result in linear branching, but instead, intersecting timelines.
But let's go through the biggest timeline problems first.
The Originals
The first four X-Men films (X-MEN, X2, X-MEN: THE LAST STAND and the prequel X-MEN ORIGINS: WOLVERINE) offer a reasonably cohesive sequence of events for the X-Men from 1979 to 2006 (with flashbacks for Wolverine going back to 1832).
However, beginning with FIRST CLASS (2011), set in the 1960s, some mild gaffes emerge: Xavier and Mystique didn't acknowledge each other in first three films but are now adoptive siblings in this prequel. FIRST CLASS also features Moira MacTaggert and Emma Frost as adult women in the 1960s... but an adult Moira was seen in the 2006 THE LAST STAND and a teen Emma was in the 1979-set X-MEN ORIGINS: WOLVERINE film.
The first meeting of Magneto and Xavier as adults does not match Xavier saying he met Magneto as a teenager and saying Magneto helped Xavier build Cerebro. And when Xavier uses Cerebro to find mutants, he sees children who look like Cyclops, Storm and Jean Grey -- who, being in their 20s and 30s in the first three X-MEN films set in the 2000s, should not even have been born yet in the 1960s (although the presence of an 18 year old Cyclops in the 1979 ORIGINS movie confuses this).
THE WOLVERINE (2013) doesn't seem to have any continuity issues with previous films, being focused on Wolverine, although Professor Xavier is shown to be alive and in his own body when THE LAST STAND implied that he had been put into someone else's body.
First Class: Reboot or Prequel?
The intention was for FIRST CLASS to be a reboot with Easter eggs cameos from the previous film series, but the sequel DAYS OF FUTURE PAST (2014) rescinds this. DAYS OF FUTURE PAST features the original cast of the first three films and the FIRST CLASS cast, making FIRST CLASS a prequel, timeline be damned. DAYS OF FUTURE PAST also shows Professor Xavier alive as he was in THE WOLVERINE with no explanation, THE LAST STAND be damned.
The end of DAYS OF FUTURE PAST shows a bright future for mutantkind in the year 2024. The original film actors are used to play the 2024 selves of the prequel actors: James McAvoy and Michael Fassbender as Xavier and Magneto in 1973 will indeed become Patrick Stewart and Ian McKellen by the 2000s, and the presence of James Marsden and Famke Janssen as Scott and Jean establishes that the child versions glimpsed in FIRST CLASS will become the adult versions of the original films.
Too Young or Not Yet Born
However, with the next X-Men film, APOCALYPSE (2016), we hit a strange situation: it's set in 1983 and features Cyclops, Storm, Jean and Nightcrawler as teenagers, but 1983 is about a decade too early; they would have been a decade older in the original films if they were teens in the 1980s. This might be dismissed as the original cast not playing their actual ages.
But even more peculiar: the winged mutant Angel is a teenager in 1983 -- but the character was already in the 2003-set THE LAST STAND, and he was a teenager there too. At this point, APOCALYPSE is showing characters in 1983 who should either be much younger or shouldn't even exist yet, and there's no reason why the time travel adventure of DAYS OF FUTURE PAST would make people exist earlier and still synchronize with the 2024 happy ending of DAYS OF FUTURE PAST.
That said, X-MEN (2000) claims to be set in "the near future", not 2000, but claiming it takes place after 2000 would mean that the APOCALYPSE characters should be even younger.
Then we come to the 2016 DEADPOOL movie which features a version of Deadpool that is separate from the version seen in X-MEN ORIGINS: WOLVERINE. In addition, Colossus, who previously appeared as a teenager in X-2 (2003), is shown as an adult in this 2016 film, but Colossus now has a heavy Russian accent. Presumably, DAYS OF FUTURE PAST meant that Deadpool and Colossus had different lives, and these contradictions are justified.
The Logan Outlier
The next continuity peculiarity is LOGAN, a 2017 film set in 2029 which tells the story of Wolverine's death. The movie confusingly claims that no new mutants have been born since 2004 thanks to X-gene suppressants in the food supply, and that all the X-Men aside from Xavier and Logan are dead due to Xavier losing control of his powers. This simply does not track with the DAYS OF FUTURE PAST 2024 ending showing mutant children as young as 10 at the X-Mansion, and Wolverine and Xavier are made up to look much older than five years.
There doesn't seem to be any explanation for how Wolverine's mutant powers and healing factor, as strong as ever in even in the dark future of DAYS OF FUTURE PAST's 2023, is suddenly failing in 2029 when Logan has been alive since 1845 and healed from all injuries. (We'll come back to this later.)
Director James Mangold insisted that LOGAN was set after DAYS OF FUTURE PAST while actor Hugh Jackman said that LOGAN was set in a parallel timeline.
Then we come to DARK PHOENIX (2019), set in 1992... where Xavier and Magneto still look like the youthful James McAvoy and Michael Fassbender even though we're only eight years away from the 2000-set X-MEN movie where they looked like Patrick Stewart and Ian McKellen. Xavier and Magneto are far too young and Scott and Jean are a little too young. McAvoy and Fassbender were playing the 60s versions of Xavier and Magneto in FIRST CLASS (2011), and have only aged eight years by DARK PHOENIX (2019) while the 2019 film is set three decades after FIRST CLASS.
Too Early or Too Soon?
DEADPOOL II further confuses things: set in 2018, we see Deadpool exploring the X-Mansion wondering where the X-Men are. One shot of the X-Men team shows that they're avoiding him -- and the shot shows the young X-Men of APOCALYPSE and DARK PHOENIX when the 2018 film should in fact show the adult cast of the original three movies. Also strangely, despite DEADPOOL II being set in 2018, Deadpool refers to the death of Wolverine in LOGAN which was established as 2029.
DEADPOOL & WOLVERINE (2024) further confuses things: set in 2024, it declares that the events of LOGAN and Wolverine's death have already happened, even though this third Deadpool film is set five years too early for Logan to be dead.
Furthermore, referring to the events of LOGAN as being in the past, the second and third Deadpool movies both feature Negasonic Teenage Warhead, Colossus, Yukio, all X-Men at Professor Xavier's school. This is despite LOGAN declaring that all of Xavier's students were dead, that no X-Men aside from Wolverine and the Professor were still alive, and the X-Mansion was no longer in operation. This simply doesn't track with all three Deadpool films presenting the X-Men as being at their 1970s - 1990s ages (somehow) and with the X-Men being very much an active superhero team and school.
What the hell is going on here?
Why do the prequels fail to line up with the originals? Why are characters born too early in the prequels? Why are characters duplicated? How can mutant births have been suppressed since 2004 when the X-Mansion is filled with young teen mutants in 2024? How can the X-Men be dead and their team shut down in LOGAN only for the second and third Deadpool films to refer to Logan's death as a past event while featuring an active X-Mansion and three young X-students?
Time Travel
The answer seems to be in two parts. First: there's time travel in DAYS OF FUTURE PAST to change the future. And in DEADPOOL II (2018), Deadpool gets his hands on a time machine which sends him to alternate timelines as well as back and forth on his timeline. He saves his girlfriend Vanessa and his friend Peter from death. He then crosses into a parallel universe and shoots actor Ryan Reynolds dead before Reynolds can perform in the GREEN LANTERN movie. He crosses into the X-MEN ORIGINS: WOLVERINE film and kills his alternate counterpart.
In the extended cut, Deadpool then goes back to 1889 and attempts to kill an infant Adolf Hitler in a maternity ward. Deadpool has clearly been engaged in extensive changes to the timeline (whatever the hell that timeline even is).
There's a lot of time travel here, and non linear thinking offers a theory.
Batman Displays His Knowledge
And in a separate universe, those of us who watched THE FLASH (2023) were treated to an interesting scene where Batman (Michael Keaton) explains time travel to Barry Allen.
BATMAN: "You're from an alternate timeline?"
BARRY: "Yes."
BATMAN: "In which you and I are friends?"
BARRY: "Yeah, you're -- you're, like, probably my best friend."
BATMAN: "Yeah?"
BARRY: "Well, but you're a bit -- You're, uh... Chronologically different. Older. And that-- that's what I can't understand; I traveled back in time from here to here, and yet somehow, everything's all changed... back here. Like, when you were born, so --"
BATMAN: "Well, time isn't linear, right?"
BARRY: "Right."
BATMAN: "At some point, you probably saw a movie that told you that if you went back and changed the past, you'd create a kind of a branched timeline."
(Batman holds up two strands of uncooked spaghetti. He places them on the table, side by side in parallel.)
BATMAN: "New present. (lightly bending the second strand to curve away from the first, creating a Y shape) And new future."
BARRY: "Yeah."
BATMAN: "Well, time doesn't work like that. That's not how time works. When you go back and change the past, you create a fulcrum."
(Batman re-positions the spaghetti so that instead of forming a Y-shape, they now intersect on the table and form an X-shape.)
BATMAN: "You put yourself on a whole 'nother strand of spaghetti. New future. New past. It's retrocausal. Echo goes both ways. Actually, echoes many ways. What you did was: you changed the future. And you changed the past. If a person is stupid enough to mess with time, what you eventually end up with is the multiverse. Some strands runs almost parallel. There will be inevitable intersections. And others that are just wildly divergent. What it is --"
(Batman pours a pot of cooked spaghetti into a bowl, the strands now curved and intertwined with each other in layers throughout the bowl.)
BATMAN: "Is a hot mess."
(Batman pours spaghetti sauce on the pasta.)
I suspect Batman's explanation of why changing the past changes time in both directions applies to the FOX X-Men 'universe' which, as Batman would point out, has become a multiverse. Batman offers a theory of time travel where branches do not form a Y shape, but instead form an X and then see multiple Xes -- intersections -- resulting from time travel.
Batman's implication is that when Barry changed the past by saving his mother, he 'rotated' his original timeline, causing it to intersect with the universe of the 1989 BATMAN movie, leading to Ben Affleck being replaced by Michael Keaton. When Barry changes the past again at the end of THE FLASH, he rotated the timeline once more and it now intersected with the timeline of BATMAN AND ROBIN (1997) and Keaton was replaced with George Clooney.
Parallel Lines
My guess is that the X-Men 'timeline' is actually five different timelines, and every odd shift in the film is due to Wolverine and Deadpool's changes causing temporal rotation.
The first X-MEN timeline is the first three films (X-MEN, X2, THE LAST STAND and the first two Wolverine films (X-MEN ORIGINS: WOLVERINE and THE WOLVERINE). This first timeline also includes the dark future scenes of DAYS OF FUTURE PAST in which the X-Men are on the losing side of the human-mutant war as the Sentinels are exterminating all mutants.
The second timeline is FIRST CLASS, and this timeline is a parallel reality from the first timeline. This second timeline has a different version of Xavier's childhood (Mystique) and Xavier and Magneto's friendship. This second timeline has Cyclops, Storm and Jean already young children in the 1960s.
Temporal Rotation and Temporal Intersection
When Wolverine travels from the dark future of DAYS OF FUTURE PAST to 1973 to prevent the Sentinel program, Wolverine finds himself in a past that is now a combination of the first and second timelines, the result of temporal rotation. Merely occupying his past self's body has led to a temporal intersection between the first and second timeline. Xavier and Magneto's lives, pre-1973, have had the first timeline's version replaced with the version in the second timeline.
When Wolverine changes the past so that the Sentinel program is prevented, there is a second instance of temporal rotation. In addition to creating the happy 2024 ending where mutantkind thrives, the timeline has now intersected with a different X-Men timeline in which Scott, Storm, Jean, Angel, and Nightcrawler were now born in the 70s and teenagers in the 80s, creating a third timeline.
Children of the Atom
Then we have the time travel events of DEADPOOL II. Each instance of time travel and each instance of Deadpool changing history has rotated the timeline and created a new intersection each time. As a result, DARK PHOENIX sees the third timeline intersect with an alternate timeline. An alternate timeline in which, I theorize, the radiation that empowers mutants was released at greater magnitudes in the 1960s.
In FIRST CLASS, the mutant Sebastian Shaw declares: "We are the children of the atom. Radiation gave birth to mutants. What will kill the humans will only make us stronger." I would suggest that increased radiation exposure in this timeline means that mutants in this version of reality age at a slower rate than in previous timelines.
I would further suggest that LOGAN is set in a timeline where the radiation that created mutants was significantly lower than in other timelines, meaning Logan's healing factor in this timeline never reached the higher peaks of alternate Logans.
Final Timeline
Because DEADPOOL II has Deadpool travel and alter history so many times, the events of LOGAN, which are set in a parallel universe, begin to intersect with the current version of the X-Men universe.
As a result, we now have a fifth timeline which includes a slightly different version of the events of LOGAN, one where Wolverine gave his life to save Laura Kinney -- but in a universe where X-Men team are very much an active superhero team and school with Negasonic Teenage Warhead and Yukio and Colossus, and mutants are still being born.
Presumably, the Logan of this timeline was exposed to some X-gene suppressant that prevented him from healing after saving Laura.
As a result, DEADPOOL & WOLVERINE is set after Logan died to save Laura, but the X-Men and Professor Xavier are still around, and they're aging very slowly (as indicated by James McAvoy playing Xavier in DEADPOOL II).
Anyway. Batman's theory of temporal rotation and intersection is what I'm going with.
If you read all of this, I owe you a Coke.