Right, I really need more sleep but can't stop thinking about this
Not sure what Annie did to end in in Gene's world, but think Sam was about leaving his partner in trouble.
Episode 1 LOM, he dumps Maya and is not willing to listen to her or her theory of who their killer is, so she goes off on her own and gets kidnapped / killed!
Last episode LOM, when Annie (and the others) need him to work with them, he runs off and goes back to 2006, but then choses to go back and save them, and he is therefore redeemed
So the writers really did have this as their background story all the way along! Genius
The more I think about Alex, the more I'm convinced Gene gave her up for her own good In the Litton episode, when the bad guy at the beginning is running away, Alex is pointing her gun and Gene says something like "going to shoot him? No, thought not" and then they both get in the car to run him over. Implying Alex doesn't shot people.
Then in this episode once Alex knows its Gene's world and they are on the air strip, she does shot her gun at the bad guys
I think this means Gene knows she is at risk, and he needs to make sure she goes to heaven before she is at risk from Keats.
Although the romantic in me does wish they had made it clearer that Gene was committing the ultimate act of love "if you love her enough Gene give her up to keep her safe / ensure she has a good eternity".
Of course I could just be writing complete rubbish, but it is making me feel better about them not ending up together