The first thing to do when entering the Subterranean docks is to clear the outside areas, but be aware there's a window into the dining hall, and you'll be attacked from in there if you're in the line of sight of those inside.
Once you've cleared the outer areas, go into the building. There's a Rogue Mage and a couple other cult members in the first room, and an Evil Priest, also with backup, in the second room. Once you've killed everyone you can read the book in the first room to see just how nuts this cult is.
Check the southwest corner for a secret room where you can pick up some coins and a few potions. Once you've done that head out and board one of the boats at the dock.