I've barely scratched the surface so far in the DB questline, so no worries about me feeding spoilers. But I can, regardless, add a thought about justifying quests(lines) that seem tenuous in a given roleplay: backstory combined with remembering that the character knows less about the world than you do. In otherwords, being naive, misinformed, or idealistic often means we do things that seem off-kilter morally/ethically.
My current character, e.g., doesn't exactly like killing. But her backstory (a loooong story going back generations) involves a certain ideology associated with the DB. However, now that she's joined, her idealism (and associated naivety) are beginning to wither. Where she goes from here, well, depends upon how *her* story plays out. The beauty of TES is that you can abandon any questline whenever you want and there's still a whole world available as a backdrop to your character's story.
