After starting with a trilogy of X-Men projects released in 2000, 2003 and 2006, 20th Century Fox’s development of X-Men spinoffs, prequels and reboots drastically confused the timeline of Fox’s X-Men Universe. This created many plot holes that persisted throughout the franchise, and led to more questions than answers being delivered in many of the X-Men movies. With Marvel Studios’ Deadpool 3 marking the returns of several X-Men characters, including Ryan Reynolds’ Deadpool and Hugh Jackman’s Wolverine, it’s possible some of these questions will be addressed, but many more will simply be forgotten, allowing the MCU’s highly-anticipated X-Men reboot to start afresh by bringing these iconic characters into the MCU.

10What Was Mister Sinister Planning?

Es𝑠e𝑥 Corp Was Teased Throughout Fox’s X-Men Franchise

For several years, 20th Century Fox teased the debut of iconic Marvel Comics villain Mister Sinister into the X-Men franchise, but the terrifying villain never actually got a chance to appear. X-Men: Apocalypse ended with Es𝑠e𝑥 Corporation agents collecting Wolverine’s blood, Deadpool 2 saw Russell held with other mutants at Es𝑠e𝑥 House for Mutant Rehabilitation, and The New Mutants’ Cecilia Reyes worked for the Es𝑠e𝑥 Corporation. Each of these teases hinted at the mutant geneticist Nathaniel Es𝑠e𝑥 making his grand entrance, but this didn’t come to pass before the end of Fox’s X-Men Universe, though there is speculation that Mister Sinister will be a prominent X-Men villain in the MCU.

9How Is Jean Grey Alive In X-Men: Days Of Future Past?

Jean Grey Died In 2019’s X-Men: Dark Phoenix

Jean Grey’s storylines in Fox’s X-Men Universe provide a clear example of the franchise’s confusing and sometimes contradictory timeline. After initially meeting her demise in X-Men: The Last Stand, Jean Grey was revived following Wolverine’s time travel antics in X-Men: Days of Future Past, which was set primarily in 2023. However, the 1990s-set X-Men: Dark Phoenix ended with the younger Jean Grey sacrificing herself to thwart the villainous D’Bari, roaming the cosmos as the Phoenix Force without a corporeal body. Jean Grey’s death in Dark Phoenix made her appearance as an adult in Days of Future Past curious, but it seems it will never be revealed how she actually survived.

8How Did William Stryker End Up With Wolverine In X-Men: Apocalypse?

William Stryker Was Revealed To Be Mystique In 2014’s X-Men: Days Of Future Past

X-Men: Apocalypse saw young members of the X-Men infiltrate William Stryker’s base of operations and release Wolverine. While this Wolverine action was brilliant, it was also confusing, as it has never become clear exactly how William Stryker got his hands on the clawed mutant. At the end of X-Men: Days of Future Past, Wolverine is fished from the river and taken into the custody of William Stryker, but the villain reveals himself to actually be the shape-shifter Mystique in disguise. Subsequent Fox X-Men projects didn’t explain how Wolverine was obtained by Stryker, and even though Hugh Jackman is returning in Deadpool 3, it’s likely this storyline will simply be forgotten.

7What’s Next For The New Mutants?

2020’s The New Mutants Was Fox’s Final X-Men Movie

The New Mutants marked a disappointing end for Fox’s X-Men Universe in 2020, after suffering from a tumultuous production period during the COVID-19 pandemic and Disney’s acquisition of 20th Century Fox. Intended to lead into an expansion of the X-Men franchise, The New Mutants’ open-ended conclusion raised the question about what would happen next for the newly-formed mutant team. Unfortunately, this will never be explored, as the project released after the cancelation of Fox’s franchise, and these versions of the characters likely won’t make the move to the MCU, leaving the team’s next steps following their battle at the hospital unclear.

6How Did Kitty Pryde Get Her Time Travel Ability?

Kitty Pryde Sent Wolverine Back In Time In 2014’s X-Men: Days Of Future Past

Elliot Page portrayed Kitty Pryde, a.k.a. Shadowcat, in Fox’s X-Men Universe projects, including X-Men: The Last Stand and X-Men: Days of Future Past. Initially seen with her Marvel Comics ability of phasing through solid objects, Kitty Pryde demonstrated the power to send others’ consciousnesses back in time in Days of Future Past, and while this allowed her to send Wolverine back in time to save the world, the origins of this power were never explored. This isn’t an ability Shadowcat demonstrates in Marvel Comics, and received no explanation whatsoever in Days of Future Past, and since Kitty Pryde didn’t make any further appearances, this will probably never be explained.

5What Happened To The X-Men Professor X Didn’t Kill Before Logan?

Professor X Killed 7 Members Of The X-Men Before 2017’s Logan

2017’s Logan is widely regarded as one of the strongest projects in Fox’s X-Men Universe, as it explored a more character-driven story featuring Hugh Jackman’s James “Logan” Howlett, Patrick Stewart’s Charles Xavier and Dafne Keen’s Laura, a.k.a. X-23, Wolverine’s biological daughter. Set in 2029, Logan revealed that Xavier’s dementia affected his telepathic ability and caused him to suffer from massive seizures, one of which killed 600 civilians and seven X-Men members a year prior. One thing Logan doesn’t explain, however, is what happened to the other members of the X-Men, as there were many students at Xavier’s School for Gifted Youngsters in the 2023-set Days of Future Past.

4Was Jean Grey The Phoenix Before X-Men: Dark Phoenix?

Jean Grey Used Her Phoenix Powers In 2016’s X-Men: Apocalypse

Sophie Turner’s Jean Grey absorbed the Phoenix Force during a mission to space in the opening moments of X-Men: Dark Phoenix, enhancing her natural telepathic abilities, while also gifting her new cosmic powers. While this was surely the first time Jean Grey had been known as the Phoenix, though, X-Men: Apocalypse saw the young mutant omit a phoenix-shape while using her abilities in the final battle against the villainous Apocalypse. This timeline confusion will probably never be explored again, as Jean Grey will surely be reinvented for the MCU, though there is still a great deal of confusion concerning 20th Century Fox’s handling of Marvel Comics’ Dark Phoenix Saga​​​​​​​.

3Why Didn’t Any Of The X-Men Age?

Fox’s X-Men Franchise Had Many Timeline Discrepancies

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While there were huge discrepancies in Fox’s X-Men Universe, one of the biggest was the fact that characters in the X-Men prequel/reboot projects never seemed to age. X-Men: First Class was set in 1963, but by the time X-Men: Dark Phoenix rolled around, exploring the 1990s, the X-Men had barely aged a day. Obviously, these projects were only produced eight years apart, but spanned thirty years, so more drastic changes should have been seen. This could have been explained as mutations causing elongated lifespans, but even Rose Byrne’s human Moira MacTaggert barely aged between First Class and Apocalypse, so the MCU should pay more attention to these small continuity details.

2How Did Professor X Come Back To Life After X-Men: The Last Stand?

Professor X Was Killed By Jean Grey In 2006’s X-Men: The Last Stand

Back in 2006, 20th Century Fox made their first attempt at adapting Marvel Comics’ Dark Phoenix Saga, but flustered completely. Famke Janssen’s Jean Grey unlocked the Dark Phoenix persona in her own body, rather than absorbing a cosmic force, and this darkness led to her making some questionable decisions, such as killing Professor X and joining Magneto’s cause. Despite his death in X-Men: The Last Stand, Patrick Stewart’s Professor X returned at the end of The Wolverine and in X-Men: Days of Future Past as if nothing had happened – in the same body. Fox’s X-Men Universe never explained how this was possible, and this will probably never be answered.

1Did Laura, A.K.A. X-23, & Her Friends Make It To Safety?

Dafne Keen Played X-23 In 2017’s Logan

Wolverine and Charles Xavier spent much of 2017’s Logan trying to get the young mutant Laura to safety, driving her to the Canadian border where she met up with other young mutants – all products of experimentation and cloning at biotechnology corporation Alkali-Transigen. After Logan’s emotional death, Laura and her new superpowered friends make their way across the border, hoping to find safety. Since Logan was produced as a standalone project, it’s possible the next steps of this storyline would have never been explored anyway. There has recently been speculation that Dafne Keen could return as X-23 in the MCU’s X-Men projects, though Marvel Studios hasn’t yet provided confirmation.