As all of you know, X-Men: Days of Future Past is the last X-Men film to feature the original team. That's because Days of Future past marks the end of the original timeline (or the original movies we started with i.e. X-Men, X2 etc.). To make everything more clear to everyone now that Wolverine's story as come to an end, I'll elaborate and explain the X-Men timelines.
Original timeline:
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End Credits scene of Days of Future Past: Apocalypse assembles the pyramids
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X-Men: Apocalypse: Apocalypse is betrayed by the horsemen and put to rest
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Opening scene of X-Men Origins: Wolverine
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Opening credits/montage of X-Men Origins: Wolverine
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Opening scene of X-Men: First Class (Magneto's mother is killed by Shaw)
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Opening scene of X-Men: First Class (Xavier meets Raven)
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Opening scene of The Wolverine
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X-Men: First Class
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X-Men: Days of Future Past: Magneto/Bullet/JFK Assassination
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X-Men: Days of Future Past: Mystique assassinates Trask
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X-Men: Days of Future Past: Xavier down in the dumps/School shut down
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X-Men Origins: Wolverine: Logan quits Team X
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X-Men Origins: Wolverine: Logan goes through his various Team X members leading him to take on Stryker and his creation Weapon XI, Deadpool. Logan kills Deadpool and gets amnesia as the result of Stryker shooting him with an adamantium bullet.
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Opening of X-Men: The Last Stand: Xavier and Erik recruit Jean Grey
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X-Men
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X2: X-Men United
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X-Men: The Last Stand
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The Wolverine
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The Wolverine after credits scene
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X-Men: Days of Future Past: The X-Men send Wolverine back in time
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X-Men: Days of Future Past: Sentinels arrive and kill the X-Men
Wolverine being sent back in time marks the end of this timeline. Either Wolverine succeeds and this timeline is erased anyway or he fails and all the X-Men die. We know he succeeds so...
New Timeline:
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End Credits scene of Days of Future Past: Apocalypse assembles the pyramids
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X-Men: Apocalypse: Apocalypse is betrayed by the horsemen and put to rest
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Opening scene of X-Men Origins: Wolverine
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Opening credits/montage of X-Men Origins: Wolverine
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Opening scene of X-Men: First Class (Magneto's mother is killed by Shaw)
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Opening scene of X-Men: First Class (Xavier meets Raven)
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Opening scene of The Wolverine
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X-Men: First Class
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X-Men: Days of Future Past: Magneto/Bullet/JFK Assassination
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X-Men: Days of Future Past: Xavier down in the dumps/School shut down
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X-Men: Days of Future Past: Wolverine comes from the future to stop the assassination of Trask and bring the X-Men together
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X-Men: Days of Future Past: Wolverine, Xavier, Hank, and Quicksilver get Magneto out of jail
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X-Men: Days of Future Past: Wolverine tells Xavier to be on the look out for Storm, Cyclops, and Jean
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X-Men: Days of Future Past: 60s Wolverine meets Stryker
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X-Men: Days of Future Past: Magneto issues a statement about the mutant race
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X-Men: Days of Future Past: Mystique DOES NOT kill Trask
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X-Men: Days of Future Past: Stryker takes Wolverine and begins Weapon X (For continuity issues, we pretend Stryker was never Mystique)
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X-Men: Apocalypse: Apocalypse wakes up
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X-Men: Apocalypse: Cyclops and Jean are recruited
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X-Men: Apocalypse: Jean releases Wolverine from Stryker's experiments and restores his memory
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X-Men: Apocalypse: The X-Men defeat Apocalypse
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Deadpool (The Wade Wilson scenes, before transformation, take place in 2014. After transformation takes place in 2015 and 2016)
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Ending of X-Men: Days of Future Past: Wolverine's memories from the original timeline catch up with him. Professor X and Wolverine are the only people that remember the original timeline. Year 2023
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Logan: Xavier has a seizure that kills 7 X-Men
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Logan: Zander Rice wipes out the remaining mutant race
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Logan: Logan and Xavier meet Laura. Year 2029
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Logan: New Mutants emerge and team up with Laura
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Logan: Logan is killed by X-24
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Logan: Laura stays with the New Mutants and fights for mutant kind
In Days of Future Past, Hank explains the time ripple theory. Everything will eventually end up the same no matter what. Thus, explaining the sword in Logan. Logan eventually did travel to Japan and meet Mariko, it just probably didn't go the same way as it did in The Wolverine. The holes in the new timeline will be filled when X-Men: Supernova is released and New Mutants, Deadpool 2, and X-Force will continue the story.
Did this help at all? Do you have any questions? Do you have something to add? Talk in the comments below