Just about everything that happens to the main Continental factions (Nauts, Coin Guard, Theleme, and Bridge) during the game is shown to you in the prologue.
Nauts: Prologue: Jonas gets kidnapped by a member of the Congregation. Main Game: Nauts get kidnapped by Coin Guard (seizing the ship, but it still counts), Theleme, and Bridge during the different quests.
Theleme: Prologue: They want you to find and turn over the heretics who are really just historians who found something that went against canon. Main Game: You help theologians discover things that went against canon and have to decide if this gets turned over or not.
Bridge: Prologue The man first gives out a fake panacea and then you learn he is running because he spoke out against experimenting on prisoners. Main Game: They send you on a wild goose chase for a panacea and then you have to stop an evil bastard from experimenting on prisoners.
Coin Guard: Prologue: You have to smuggle things for the Coin Guard. Main Game: There is a criminal organization inside the guard that smuggles slaves and alcohol and you have to stop it. (this is a little more of a stretch because your smuggling in the beginning is actually somewhat related to this).
It is pretty impressive how they got almost every main plot idea into the prologue missions.