Your dad wasn't in tranquility lane. Does the game actually force you down into that vault? I can't remember anything like that. There's also the thing about killing treeguy or not. Pretty sure that was unrelated to the dad plot as well.
-edit- so i was wrong, the area wasn't optional, but how you decided to solve it didn't have a very tangible effect ont he game world, except the dumb karma system reacting to it. a system that shouldn't really have been in the game at all
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