So here's what happens: there's this scientist lady, and she's researching the evil but sort-of-not-evil aliens in her lab. She wants something from you and you can decide whether to trust her. If you decide that she's alright, then you do some mission, get a reward, and she lives happily ever after, never to factor into the plot again. If you decide you don't like her and suspect something is up, it turns out she was an alien sleeper agent and you were right not to listen to her, and she gets killed and the game goes on no different. The idea is that whichever choice you make, the narrative world alters to make it the right one.
This is the epitome of wish-fulfillment storytelling, where the player can do no wrong. Not every game is guilty to this extreme, but I shake my head in disgust at those that cross the line.