Spoilers.
Finally finished the game. Towards the end it got repetitive. The character is probably one of the worst characters I've ever played as. The voice actor was good, however.
I spoiled the ending for myself and read that you can kill both people (forgot their names). I shot the the girl, mainly because there isn't an option to romance her. Probably one of the best looking female characters in gaming history and you can't romance her?!
I let pagan live, because he's funny. I still have the game installed in case I want to come back and do more stealthy fort liberations. Also, what happened to the asian chick that was with pagan? I believe she also poisons/drugs your character and leaves you in a prison. You never see her again after that.
Somewhere there is a mission that finishes that story line. I think it's a thankga mission? It starts in a cave, but I can't remember exactly what starts the funky tease dream about Yuma. I thought Pagan Min referenced Yuma and the player later.