In order to make sense of this cinematic universe I’ve cut two movies from canon and I use a bit of head canon when it comes to his adamantium claws returning. You have to lose Origins and Dark Phoenix. Origins causes too many issues, Sabretooth being the biggest but also there’s issues with Stryker being taken for questioning for murder at the end but yet he’s clearly free in X2. You can use head canon to say Sabretooth from X1 and Creed in Origins are different people, Origins doesn’t refer to Creed as Sabretooth anywhere in the movie. But then it also gives us a terrible Deadpool. For what it adds compared to what it fucks up, it’s not worth keeping.
Same with Dark Phoenix. It ends with Jean becoming Phoenix but DOFP ends with Logan in a 2023 where Jean isn’t Phoenix. Dark Phoenix is also wholly terrible so we can ignore it.
So we end up with two timelines.
The Sentinel Timeline. In this timeline, Mystique murder Trask in 1973, causing the governments of the world to use Mystique’s DNA to develop the shape shifting Sentinels they use on Mutantkind in 2023.
In this timeline the events of X1, X2 and X3 happen. In this timeline they meet Nightcrawler as an adult. Then Logan goes to Japan to mourn Jean. At the end of The Wolverine in 2013, he has only bones claws again whilst being warned of a terrible future to come.
Here’s the head canon part. Logan had more Adamantium grafted onto his claws, Cyclops heated the metal, Magneto grafted the liquid metal onto his bone claws for the coming battles.
From here Logan goes back to his younger body and the events of DOFP play out which results in Mystique not killing Trask and it starts the “Essex Corporation/Alkali-Transigen” timeline.
At the end of DOFP, 2023 Logan returns to his changed future that seems idyllic but in just six short years The Westchester Incident will occur and Logan, Charles and Kaliban in this timeline go hide in the middle of nowhere to protect everyone from Charles.
How does Charles remember the events of Liberty Island in X1? He’s doesn’t, he’s just been told all about it by Logan and has seen the events in Logan’s memories. That’s how he seemingly knows of the Statue of Liberty attack.
Future Logan changes things in 1973 and goes back to 2023. In between that time, the events of Apocalypse happen. In this new timeline, the present day 80’s Logan is released from the Weapon X experiment by The X-Men, he goes on to eventually join the X-Men and eventually we get to the events of him ‘returning’ to his body in 2013.
Before we get to the events of Logan we have one more movie that whilst not amazing, adds a bunch of world building to this new timeline by focusing on the nefarious shit The Essex Corporation we’re doing at that time.
Apocalypse ends with The Essex Corporation getting Logan’s blood/DNA which will lead to Alkali Transigen creating Laura and X-24. New Mutants show us a glimpse of what else The Essex Corporation were doing to mutants out there between the 80’s and 2029 when we reach the events of Logan.
Logan plays out and we have an ending.
The Deadpool movies for me exist outside this cinematic universe, they’re great but Deadpool’s breaking the fourth wall stuff just causes more continuity and canon issues, plus Deadpool 2 apparently exists in canon around the time it was made and features the younger X-Men actors cameoing which breaks chronology.
The Deadpool movies are great, they also exist separate to the main narrative for me.
Same with Legion. I’d love for it to fit with the main movie series but it ends with Charles having a baby that doesn’t need sending away and therefore it doesn’t fit. Where is Charles wife and baby if Legion is in the same universe? Doesn’t work. So I keep it separate.
The Gifted I also ignore as it wasn’t very good.
So for me it’s
X1, X2, X3, The Wolverine, Days of Future Past, Apocalypse, New Mutants and Logan
Then the Deadpool movies separate but references both timelines, then Legion.