In Alien Mind, players take on the role of biologist and physicist, Timothy Hunter. Timothy has been called upon by his friend Aaron Avery to visit the research space station Zekford in order to partake in the study of two recently discovered, unhatched eggs of unknown origin. Upon arrival, Hunter soon realizes that all is not well on the space station Zekford.

Zekford has been overrun with hostile aliens--the bodies of the research scientists lying strewn about the halls. Timothy must blast his way through the hordes of enemies and solve the puzzles contained in the data left in the station's central computer system in order stop the second alien from hatching and to save his friend.

The game plays mostly as a top-down arcade shooter. The player must stay alive and interface with the various computer terminals throughout the level. These terminals provide the player with clues that allow the player to access new sections of the level. The clues come in the form of riddles that reference both the objects in the game and the back story contained in the game's manual.