Dark Phoenix clearly went through a bit of reshoots, especially in its third act finale. Apparently the original finale resembled too much of another movie, and while some have speculated that it resembles Captain Marvel, writer-director Simon Kinberg tells io9 that the original ending was closer to Captain America: Civil War:
My original ending didn’t have the entire X-Family together the way they are in the film now. More than Captain Marvel, you could see a lot of Civil War in that ending. Usually, these big, huge action movies have the climactic moment in the third act. I loved the way that Civil War had its big action action set piece where everyone’s facing off more towards the end of the second act rather than in the third, so that after that huge battle, you’re left with Winter Soldier, Captain America, and Iron Man.
It’s this telescoped down view of their raw emotions, and I loved how intimate that was. That’s what I was going for with Dark Phoenix’s ending even though it then might have looked like Captain Marvel for about two minutes.
Without giving anything away, you can still see how the film could have gone in a Captain Marvel direction near the end, but the Civil War aspect also makes sense. As the trailers have shown, this movie is about the X-Men fracturing over what to do about Jean Grey. The crucial misunderstanding that Kinberg makes is that he didn’t build up any relationships between these characters. Imagine Civil War if Iron Man and Captain America had never interacted before turning against each other. Even Civil War is sly enough to acknowledge when certain characters are fighting there might be lower stakes between, say Hawkeye and Black Panther than Hawkeye and Black Widow.
So even though Kinberg pivoted away from what would have been another X-Men movie ending with mutants versus mutants (for those keeping score, that’s the climax of X-Men, X-Men: The Last Stand, X-Men Origins: Wolverine, X-Men: First Class, X-Men: Apocalypse, Deadpool, and The Wolverine), it wouldn’t really matter because the foundation of Dark Phoenix is so fundamentally flawed.