Let me refrain that there is major spoilers ahead for the X-Men films, including Logan. As Wade Wilson said in his film, Deadpool; "McAvoy or Stewart; these timelines are so confusing". Wade does make a point that all of us viewers and fans have bemoaned since X-Men: Days of Future Past which effectively rebooted the series while keeping the cast mostly intact.
Let's break the events down:
1845: James Howlett (Logan) kills the man who turns out to be his biological father and escapes with his brother, Victor aka "Sabertooth". This is the intro to X-Men Origins: Wolverine.
1944: Young Magneto is a child in a German concentration camp. His parents are murdered by Sebastian Shaw. This is the intro to both the first X-Men film and is explored in depth in the intro to X-Men: First Class.
1945: Logan is in P.O.W. camp in Nagasaki, Japan. Logan saves Yoshida. Yoshida thanks Logan and goes on about his business rebuilding Japan and his empire. This is the intro to the Wolverine. It is also worth noting that Victor and Logan must have been off fighting in different parts of WWII at the time as Victor is nowhere to be seen. However we do know that both of them fight together side-by-side in various other conflicts.
1962: Professor Xavier and Mystique meet Moira McTaggert and form a bond with Magneto who is out to kill Sebastian Shaw. We encounter Logan at a bar drinking. Then we have the rest of the events of X-Men: First Class which plays out.
1973: Logan, down and out from various wars is a bodyguard whom has a vision to seek out Professor Charles Xavier. Logan finds him and reveals to Charles that through another dimension in time and space, the older Xavier relays a message that Bolivar Trask must stop his sinister plans to unleash Sentinels on mutants. This is the "Past" portion of X-Men: Days of Future Past.
After this point in time, the continuity is completely altered and events are out of order. We do know that when Logan was sent back through time in the non-existent universe, he knew of all of the events from the X-Men trilogy which was altered and mentions the names of several mutants to Charles Xavier; Cyclops, Jean, Colossus, etc. This was most likely to prevent them from going astray and to possibly stop them from joining the "Brotherhood" which is Magneto's evil group of mutants.
New time line starts with Logan being taken by Mystique (in the disguise of General Stryker) to Alkali Lake to have the Adamantium bonded to his skeleton. All of the events past the opening war sequence of X-Men Origins: Wolverine has been erased and have never happened in the way we saw. We do not know if Team X existed, but, we do know from that film that Stryker was in Africa mining for the Adamantium. And we all know that he needed that for the "Weapon X" program.
Discrepancy is Wade Wilson. If the Vietnam sequence is indeed around 1975 at the end of the war, that means he'd probably be around 20, meaning that he would be 61 in Deadpool. We will just assume that Wade Wilson had a son who would also be called Wade and would go on to become Deadpool at a later point in time. There would be no "Weapon XI" in this timeline.
1983: The "first" mutant, Apocalypse; is awoken after sensing the time and space paradox being distorted from the events in Days of Future Past. The events unfold in the film, X-Men: Apocalypse. Logan appears and has just gone through the Adamantium bonding process and escapes the facility as he is freed by young Scott and Jean as they search for the Professor and the rest of the kidnapped students.
2000: From the film Logan, we know that from what Charles Xavier says, Logan still came the school and the events at the Statue of Liberty still occurred. In what way, we don't know.
2004: According to the film, Logan, last known mutant was born in 2004.
2013: From the film, Logan; we see a Samurai sword on the wall when he is in Mexico. Since the events have been altered, Yoshida would have been unaffected as he was on the other side of the world in Japan building his empire. We don't know if or how these events were altered, but, we do know that in some way, the events of the Wolverine had happened. Granted, Logan would not have been haunted by the memory of Jean Grey since she is still alive and the events of X-Men: the Last Stand did not happen.
2015?: Logan wakes up in the present at Xavier's school. As he wakes up and tries to understand what is happening, he sees all the familiar faces of those who died or left the school. He sees Rogue, who left the mutant life behind in the Last Stand. Logan is shocked to see both Jean and Scott still alive and well. Logan goes to the Xavier and they both seem to have a mutual understanding that they both know that time and space has been altered. This is the end of Days of Future Past.
2016: The events of the film Deadpool play out.
2018: From the film Logan, Laura aka X-23 is born in Mexico sometime in 2018.
2029: Logan.
Speculations from Logan; it is possible that Charles Xavier killed a large majority of mutants in the United States from his Alzheimer/degeneration of his brain. This most likely was strong enough to kill Magneto. Whatever this event was, it cause Logan to take Charles on the run and take care of him until he dies. However, as strong as this event was, it did not have the ability to reach out to Mexico to kill the mutants there. Therefor, it did not kill Laura and the others. Obviously, from the fourteen years after the end of Days of Future Past, Logan has moved on from Jean.
Since Scott and Jean lived and the events of the Last Stand did not happen; the potential for them to conceive Nathan Summers aka Cable is most likely. Especially since Deadpool has been breaking the fourth wall and makes mention of Cable being present in Deadpool 2.
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