On Level 1 (Nightbreed), Boone must deal with the Sons of the Free, Mask, Lude and Neckend among others before descending to Level 2 (Midian)
Once in Midian, Boone must enter Baphomet's Chamber and free the Breed. Meanwhile... Mask has kidnapped Lori and Boone must return to Necropolis to save her...
Level 3 (Rope Bridge) sees Boone rescue Lori and release the Beserkers.