It's started at the Halted Stream camp. I replace some of the NPC's as Haled Stream bandits being attacked by a horde of hired mercenaries. Throughout this three way fight (or sneak in) you come across the same set of NPC's, but have a captive prisoner that is in need of rescuing. After rescuing her, you learn of the BlackWater gang that she was in and how she was disbanded, along with being looked at as a traitor. The player will also learn these mercenaries for hire were also destined to kill her, along with the buyers whom are the bandits at Halted Stream (pretty much a setup with no strings attached or hands being dirty)
Throughout the quest, the player must search for the NPC's sister and save her. After saving her, both NPC's become the players followers if permitted. If not, I want to transport them to the rorikstead inn where they can hangout until the player needs them (so I think a script for this one?)
Other than that, that's pretty much it. started game enabled as in pop up? If so, then yes. As for the SEQ file, I'm not quite sure what you mean.