The game begins with Roger Wilco facing trial for his actions during the previous game, Space Quest V. He is demoted to a second-class janitor aboard the SCS DeepShip 86.
Later, Commander Kielbasa of the DeepShip awards the crew shore leave on the planet Polysorbate LX while an elderly woman named Sharpei plots Roger’s demise. Sharpei intends to use Roger’s body to extend her own life as part of ”Project Immortality.”
Roger is rescued several times by Stellar Santiago, a humanoid alien who is a friend and love interest to Roger. Eventually, Sharpei manages to capture Stellar instead and attempts to use nanites to transfer her consciousness into Stellar’s body. Roger uses miniaturization technology to shrink to a tiny size and thwart Sharpei’s nanite robots from within Stellar’s body.
The game concludes with Roger and Stellar reunited and Stellar hinting at Roger’s ”next assignment.”
