You get quests from Preston (Maybe promote him to Admiral or something, so that it makes more sense that he orders a general around), and from time to time a courser appears, with whom you have to talk, without getting caught by the regular settlers.
You replace the general and are supposed to play along. Maybe to Sanctuary, only this time, it's populated by the Minutemen already. You don't get an actual pip-boy, instead it's always the powerarmor-style overlay. Also, there is this 'easter egg' in one of the terminals at the institute where they are talking about basically integrating a pip-boy into a synth. You pick a gender, some traits, use some configuration terminal to select the synth's face, then the synth gets made.
You start as some institute scientist in that synth fabrication room.
There are a few Alternative Start mods, and there is some discussion here whenever the protagonist is a synth or not.
