Zeta is an adventure game with light dungeon crawling elements. The star ship Pilgrims is sent to investigate an accident on the planet Z (or Zeta-3) in the Zeta star system, and find out what happened to the first investigation team sent earlier, and to search for the lost transport ship Sanctuary.

A development base on Z was destroyed under mysterious circumstances 100 years ago, which is suspected to be related to the more recent disappearances. Players take control of crew member Kou Asamiya aboard the Pilgrims, as it encounters an emergency in an asteroid belt, and some crew members appear to suffer from memory loss.