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Logan was no stranger to violence and heartbreak, with its R-rating allowing for it punch movie-goers straight in the gut. However, even with all the blood it splatters in its runtime, the original opening of Logan might have have been too much. A hovering question in Logan is what happened to the X-Men, before we learn how Professor X contributed to their death. Well, director-writer James Mangold had initially planned to have the death of the X-Men as the very first scene of the movie, killed accidentally by their own teacher.
When Logan opens, it's just Logan, Charles Xavier, and Caliban against the world. Mutants are dying out, and Logan is essentially just waiting until he can finally let go too. A brain disorder has left Xavier a shell of his former self, occasionally sending him into an uncontrollable telepathic spasm that hurts anyone close by. While it is never overtly said, it is strongly implied that one of these spasms occurred at the X-Mansion and killed several of the X-Men. James Mangold told IGN that this was the scene he wanted to begin the movie with.
With that reasoning, it makes total sense why they decided to drop the scene. It makes the movie less about Logan and more about the death of the X-Men. The incident works fairly well living in the background, and isn't totally necessary to understand where Logan and Charles are emotionally. Plus, starting a movie with the death of recognizable characters is really depressing. While Logan is no smile party, I don't think anyone needed the movie to start off that way.
This death of the X-Men in Logan brings to mind the way the team met their end in Old Man Logan, the comic book storyline that inspired the film. In that alternate universe, all the supervillains teamed up to defeat the heroes and take over America in one swoop. Wolverine found the X-Mansion overrun with villains and preceded to unleash hell, brutally killing everyone. However, the whole thing turned out to be an illusion, and Wolverine was actually killing the X-Men. It's extremely brutal, and it should be noted that it wasn't the opening of the comic but a reveal later on.
We will likely never this scene come to life, but if you have an X-Men dying itch to scratch, you could always watch X-Men: Days of Future Past. Logan is out on digital right now and its home release reaches shelves on May 23, 2017.