The PROTAGONIST, nameless, wakes up in the Bridge of the Exodus-class frigate Pan's Flight. By the time this happens, the human crew of the ship have been in cryosleep for an indeterminate amount of time. The PROTAGONIST is antagonized by the ship's on-board AI, WENDEE who seems to have gone rogue due to some as-of-yet unknown reason.
The PROTAGONIST interacts with terminals, solves puzzles, listens to audio logs, and figures out the mystery behind the Pan's Flight and the reason behind WENDEE's madness. In the end, the player must make a choice. Will it save the unknown colonists or will it side with WENDEE?