What will happen in the end? You work for a terrorist organization, hire the most ruthless individuals in the galaxy, and spread "lies" about the "Reapers." They'll send another Spectre after you, and that will be quite a spectacle. I can even imagine it: they'll definitely send a human Spectre, a naive and inexperienced one, just like Shepard used to be. "Oh, you're evil and a threat to the entire galaxy, you betrayed the Council!" (Shepard, in Saren's voice) - "You don't understand, this is for the good of everyone, it's the only way we can be saved, join me!"
Where do we end up when we save the world?