Originally Posted by Melapi
Well in the last scene Jean, not Phoenix, asked Logan to kill her. I assume Phoenix couldn't restrain Jean all the time, like in the lab, so it's easy that in the last moment Jean could told Scott to run, causing a fight for the mental blocks between Jean and Phoenix in which they could end in the unconscious state Logan and Storm found Jean/Phoenix.
It's a viable option, not being in denial.
He's dead. Face the facts. They gave him a tombstone at the end of the movie - that the writers, director and studio telling you that they intended for him to be dead.
The whole Phoenix plot hinges on him being dead - it makes her a dangerous person whose powers must be stopped.