It took a few cracks, but I did it…I made Dark Phoenix work with X-Men: The Last Stand, to function as a third in the trilogy that began with Days of Future Past and continued with Apocalypse.
-Film begins with the first fifty-four minutes of Dark Phoenix, only without the aliens popping up
-The DP footage comes to an end when Teen Jean departs Magneto’s island, from there Last Stand footage begins with the Danger Room sequence (because it has the line “the not too distant future” at the start to indicate the passage of time)
-Scott’s PTSD over Jean is now repurposed. Instead of seeing her drown, he sees her absorb the Phoenix force in space. Scott departs the X-Mansion to clear his head (we know he returns in DOFP’s final scene so we’re good)
-Logan knows of Jean in this timeline as a continuity nod to their meeting in X-Men Apocalypse. There is no romantic connection between them this time.
-Beast’s visit to the X-Mansion in the present day is now much more formal due to the tension between Hank and Charles in the past. Exchange with Logan shortened
-Instead of seeking out Mystique, Magneto seeks out Jean.
-Xavier ‘sensing’ Jean at the lake moved to after Magneto and Jean have a conversation at Magneto’s base camp. Blackbird arrives at the lake and Logan storms the camp looking for Jean. Gets involved in fights.
-Film proceeds apace, Magneto and his forces attack Alcatraz, X-Men suit up to stop them. We see Warren Worthington, but he has more of a mystery about him, now he’s just a student at Xavier’s school wanting a piece of the action and help out where he can.
-Logan and Jean’s meeting from X-Men Apocalypse inserted into his final battle with Phoenix. Memories of this allows Jean to regain control and beg Logan to save her. He stabs her.
-Jean is only wounded, not killed. We see her back at the mansion being tended to by Xavier. Teen Jean voice-over about evolution plays over Jean’s comatose body as Logan watches her. We’re led to believe Jean will recover and reunite with Scott, which we see in the final scenes of Days of Future Past.
-Last Stand ending is as normal.