- Colossus: Let us go talk to the Professor.
Deadpool: McAvoy or Stewart? These timelines are so confusing...—Deadpool (2016). While not for that exact reason, he's right.
In the process of creating prequels for the X-Men Film Series, different creative teams have introduced a number of discrepancies in the franchise in fact, the only sign they're meant to be in the same continuity is the presence of Wolverine in all but one of the films and the character of William Stryker. Almost all of the films have continuity snarls with other installments; most of the time it's a conflict between the movie trilogy and one of the other films.
The introduction of an Alternate Continuity created via Mental Time Travel in X-Men: Days of Future Past excuses some of the discrepancies, but opens up several other problems (including which of the films are or are not affected by the new timeline).
This entire thing is lampshaded profusely in Deadpool 2's mid credits scene as Wade drops in on the fight between Logan and Weapon XI (the In Name Only Deadpool) and proceeds to fill his counterpart with a lot of lead while making fun of all the continuity problems the movies have caused.
Films with their own pages:
- The process by which Wolverine received his adamantium claws changes through several films. In X-Men, dialogue and x-rays show that he had mechanical pistons and claws grafted into his arms. X2: X-Men United hints that the adamantium was injected and shaped by doctors, and (in a flashback) Logan is seen fighting off several doctors who've been working on him before escaping the Alkali Lake facility covered in blood. Additionally, Stryker takes credit for Logan's claws, seemingly confirming that they're mechanical in nature and were surgically implanted in his body. In X-Men Origins: Wolverine, the adamantium bonding process is hands-free, no doctors ever work on Logan, and the adamantium is grafted to his bone claws, something he wasn't mentioned as having in the following films (except The Wolverine, where Silver Samurai cuts the claws in half with an adamantium blade and drills into the bone marrow to leech off Logan's Healing Factor; then again, by the next movie the claws are fully metallic again). Additionally, the X-rays don't show the two giant holes he should have in his skull.
- This actually mirrors the series of retcons regarding his claws in the comics. Originally they were part of his gloves, then retconned into a result of the Weapon X experiment, then finally retconned into bone claws.
- Logan asks if he and Charles Xavier have met before, but is told by the latter that this is not the case. However, this is contradicted by First Class (where Erik and Charles approach him in a bar, only to be rudely told off). Later, in X-Men: Days of Future Past (which canonically takes place 11 years after First Class), this is given an Ironic Echo when Xavier does remember the incident and uses it as the reason to kick Logan out of the school, though he eventually relents and allows the latter to join them as they attend the Paris Peace Accord and Nixon's unveiling of the Sentinels.
- Watch Senator Kelly's "mutants are real" speech in the first film, and try to imagine that this is taking place in a universe where the government was building Sentinels thirty years earlier (in X-Men: Days of Future Past). Likewise, the Congressional discussion of the mutant gene being new and shocking is contradicted by the world's discovery of mutants in 1962, which informs Congress' decision to hold senate hearings on the matter in 1973.
- Xavier claims that he and Magneto first met when the former was 17. X-Men: First Class has their first meeting in 1962 (with Charles being 29 years old), but prior to this shows a younger Charles aged around 11, alive and well in 1944.
- Xavier also claims that before they were X-Men, Cyclops, Jean Grey, and Storm were some of his first students. The titular "First Class" of students from X-Men: First Class consists of an entirely different group of young mutants (Havok, Beast, Banshee, Mystique, Darwin and Angel Salvadore), with the X-Men from the first film presumably not even joining the school until decades later. X-Men: Apocalypse establishes that the school brought on Scott, Jean and Storm in the 80s, and that numerous students were already attending Xavier's school by that time, but still doesn't address or rectify the point.
- It is established in dialogue by Xavier that he and Erik built the first Cerebro together. First Class establishes that the first Cerebro was a CIA-owned invention partially built by Hank McCoy, and that Erik never had any direct involvement in its construction, nor the second version that was later built and operated in Charles' school (due to being imprisoned for a large part of the interim between the first and second prequel films). This may have been given an Author's Saving Throw in X-Men: Apocalypse, as Jean and Magneto are seen rebuilding the school (and presumably Cerebro) after it is destroyed in a generator explosion.
- Mystique is tasked by Erik to infiltrate the X-Mansion, sabotage Cerebro and place Xavier in a coma, but never seems to have any misgivings or regret over doing so, despite being established as Charles' surrogate sister in First Class and knowing him for several decades during the prequel films. Likewise, Charles never regards her as anything more than Magneto's subordinate. Fans can only wonder what drove the two apart in the original timeline.
- When Magneto, Toad and Sabretooth reveal themselves at the train station, Xavier is surprised and comments that Magneto's helmet is something he's never seen before, as it is blocking him from accessing his thoughts. It is also stated that Erik built his helmet around the time that Senator Kelly's Mutant Registration Act led him to ramp up the Brotherhood's terrorist campaign, since he knew that Xavier was tracking him. As First Class showed, Erik obtained his signature helmet 40 years earlier from Sebastian Shaw, in 1962, and Charles had full knowledge of it.
- Dr. Hank McCoy makes his first appearance in a background cameo, where he's seen as a human-looking scientist being interviewed on a news program. By the time he appears in X-Men: The Last Stand, however, he's a politician in the U.S. Presidential Cabinet and sports his classic blue-furred simian mutant form. First Class then reveals that he was one of the original X-Men in The '60s, when one of his experiments went awry and accelerated his mutation. This was later given an Author's Saving Throw in Days of Future Past, when Hank is shown to have developed a serum that removes his blue fur and regresses him back to a human form for brief periods of time. It also clarifies the true nature of his close relationship with Charles Xavier, establishing that he was the only one of Xavier's original students that stayed behind when Xavier shut the school down during the Vietnam War.
- Additionally, Hank's cameo shows him speaking to Sebastian Shaw. As of First Class (which takes place 40 years before this), Shaw is canonically dead due to a coin driven through his head by Erik and his corpse being thrown out of the submarine to display to the other mutants, as well as a villain, although this could have simply been a different character with the same name.
- In the opening flashback, Charles is seen as an older man who is not paralyzed and walking around (with Erik, no less) when they visit the young Jean Grey. Days of Future Past has an Author's Saving Throw stating that Hank developed a serum for Charles that allowed him to walk again (at the expense of temporarily blocking his mutant abilities). However, this doesn't explain how Charles can speak to Jean telepathically and walk at the same time.
- Likewise, it is shown that Charles and Erik are on good terms with each other, despite other films set in and around the late 70s/early 80s time period (including Days of Future Past and Apocalypse) showing them as being Vitriolic Best Buds at best. Even accounting for the Mental Time Travel in Days of Future Past, it doesn't seem very plausible that they could have patched up their relationship so quickly.
- In a possible case of Aborted Arc, the film introduces Bolivar Trask in a small supporting role as the United States Secretary of Defense, but never gives him a major role in the story. He later reappears in Days of Future Past as a major antagonist... where he's gone from a tall, middle-aged African-American military officer from 2006 to a much younger, Caucasian dwarf scientist who was assassinated by Mystique in the 1970's. There is a fan theory is that the Trask seen in The Last Stand is the adopted son of the one from Days of Future Past, making him "Bolivar Trask Junior".
- Dr. Moira MacTaggert is first introduced in a brief cameo, where she's a British scientist who has apparently been friendly with Charles Xavier for years, and played by 38-year old Olivia Williams. In First Class, which takes place four decades earlier, she's an American CIA agent played by 32-year old Rose Byrne, who has her memories of Xavier erased at the end of the movie. Even with the Author's Saving Throw established in Apocalypse (Charles restores her memories of him and they begin a relationship), it doesn't reconcile the character's accent between the two films.
- Cyclops is portrayed as a teenager in 1979 during Origins, but is portrayed as a man in his mid to late twenties in the original X-Men trilogy, which takes place 20 or so years later. James Marsden was 27 when he portrayed Cyclops in the original film, about ten years too young.
- The film features a brief appearance by Kayla Silverfox's sister, a young blond-haired woman who's clearly intended to be Emma Frost (she's listed as "Emma" in the final credits and is identified as "Emma Frost" in a TV spot). Despite this, First Class explicitly introduces Emma Frost as a major character in her late 20s/early 30s in 1962, 17 years before the events at Three Mile Island in 1979. She also has psychic powers that were never referenced in Origins, and never gives any indication that she's Kayla's sister.
- Cyclops was blindfolded whilst being rescued from Three Mile Island by Logan, but it still seems unlikely that in X1, he would have no idea whatsoever that he has met the man who once saved his life, and that no one informed him at any point afterwards.
- Like The Last Stand, Xavier is shown both walking and communicating telepathically with the escapees from Stryker's island, which also isn't fully explained by the Author's Saving Throw in Days of Future Past (the serum that allows Xavier to walk again, at the cost of temporary loss of his mutant powers). Word of God claims that this was a mental projection.
- In previous films, it had been established that Logan had no memory of his past prior to 1979. So how, exactly, was he able to remember saving Yashida during World War II? It should also be noted that this takes place prior to the Mental Time Travel/Alternate Timeline shown in Days of Future Past, and that there was no reason given for Origins to be non-canon at this point.
- The prequel comic for the first X-Men film featured the Silver Samurai as a mutant Yakuza enforcer who fought Logan shortly before the events of the movie. Harada shows up here as a normal (albeit well-trained) human with no powers, and it's clear he's never met Logan before. Instead, the Silver Samurai is Mariko's grandfather in a suit of Powered Armor.
- A justified example involving Ripple-Proof Memory. Prior to the release of the film, producer Lauren Donner Schuler went on record saying that the film made X-Men Origins: Wolverine and X-Men: The Last Stand non-canon. However, the film still references Logan's memories using scenes from X-Men: The Last Stand, and from X-Men Origins: Wolverine, namely Logan killing Jean at Alcatraz and finding Kayla "dead" in the forest. This is because it is established early on in the film that if Wolverine is successful, he will still remember the timeline that leads to the war with the Sentinels, which still exists, up until it diverges when Mystique no longer kills Trask. He himself points this by saying the history he knows is different than what new Xavier knows.
- Josh Helman's Colonel Stryker looks like a child compared to to Danny Huston's, who he would supposedly become in roughly 6 months. The actor looks the same in Apocalypse, which takes place several years after X-men Origins did in the original timeline.
- Hank invents a serum that can suppress mutations in this movie. This explains why he is seen as a normal human in X2 and how Xavier can walk during certain scenes, but creates a whole new plothole when they are shocked that a mutant cure has been developed in The Last Stand. Albeit it could just be because, unlike the serum, the cure supposedly has permanent effects.
- Bryan Singer has suggested in promotional material that several characters featured in this film as teenagers would have been born earlier, thanks to Days of Future Past rewriting the timeline. However, it's only been 10 years since the point of divergence so nobody "born much earlier" could possibly be older than 9 years old in 1983. Not to mention that Cyclops and co. look young for their age in the 2023-scene of Future Past.
- Apocalypse, which depicts Cyclops and Storm as teenagers (and played by different teenage actors, no less) during the 1980's, despite getting cameos as children in the sixties-set First Class.
- Moira acts as though she's never met Xavier before (or any of the other characters present in First Class) when he and Hank visit her at the CIA offices, and it is claimed that this is due to the mind-wiping he did to her nearly two decades prior. Yet, from her description in First Class, she claims that she doesn't remember anything after she left the CIA compound, which would mean that she would still have memories of her first meeting with Charles and Hank and their initial experiment with Cerebro. She's also shown to be made aware by her superiors that Charles did something to her that caused her memory loss.
- Raven/Mystique claims that she acknowledged the first group of students at the Institute (Banshee, Beast, Charles, Erik and herself) as "X-Men" (and said it to them) while speaking with the new group as they fly towards Apocalypse's location in Egypt. Despite this, she is never have shown to have said a thing in First Class during their mission — Moira is the first character to refer to the team as "X-Men", and that only occurs after the mission is over and she's delivering her report to the CIA brass at the end of the film.
- The Phoenix Force enters Jean after she saves the team during the space mission, and it is established that this is this is the first time the cosmic entity has done so. This seemingly disregards the ending of Apocalypse, where Jean uses what appears to be the Phoenix Force for the first time to defeat the titular villain (and the imagery showing a phoenix awakening as she hovers in the air). Various reasons have been brought up to try to explain the discrepancy, including the (comic-only) explanation that the Phoenix Force causes "flare-ups" in its host prior to full possession, but no actual explanation or reason for the snarl (from either Jean or other characters) is given within the film itself.
- Both Xavier (canonically born in 1932) and Erik (canonically born in 1930) are both in their early-to-mid 60s by the point in the timeline where Dark Phoenix takes place, but are placed by James McAvoy and Michael Fassbender, who are both twenty-plus years younger than their characters at this pointnote . While Mystique (played by Jennifer Lawrence) is shown to have slower aging genes (a trait which carries over into later films), no such excuse is given for either Charles or Erik.
- The ending of Days of Future Past establishes that Charles remained the headmaster of his academy and Jean is shown alive and well and with her friends in the school. It is seemingly contradicted by the ending of Phoenix, where Jean is presumed dead after pulling a Heroic Sacrifice to stop Vuk, and Charles retired from his position as the headmaster due to his guilt for being partly responsible for Jean losing control, leaving Hank in charge of the school - which is now renamed Jean Greys School for Gifted Youngsters. Though given that Phoenix is shown flying through the atmosphere in the ending, and that the epilogue of Days of Future Past took place decades after this movie, presumably both Jean Grey and Charles decide to return to the team during the Time Skip offscreen.