Dark Seed II continues the nightmare of Mike Dawson as he recovers from a nervous breakdown from his earlier encounters with the Ancients. Back in his hometown, Mike's high school sweetheart, Rita, is found murdered after the high school reunion. Unfortunately, Mike cannot remember much about that night, even though others saw him with Rita. Now, as the prime suspect, he must find a way to prove his innocence.

The designs of H.R. Giger are pivotal in this horror-tinged point 'n click adventure. Players will be swapping between the Normal World and the Dark World, with 75 prerendered 3D locations in total. There are 40 characters to interact with. The goal is to overthrow the Behemoth of the Dark World and cut through the corruption of the Normal World.

Movement, action and dialogue interaction modes are toggled between using the right mouse button, with the full screen used for location display unless the game menu or inventory bars are called into use.