Alien crystals come in two variations: small and large, possibly as a form of alien currency. They are only found aboard Mothership Zeta on some aliens, lying on some tables or shelves where they are especially hidden among the alien artifacts that cannot be picked up. Most quantities for both variants are found in the hangar and robot assembly.
- 39 small/large crystals in the robot assembly.
- 36 small/large crystals in the hangar.
- 13 small/large crystals in the living quarters.
- Seven small crystals in the observation deck.
- Seven small crystals in the cryo lab.
- Seven small crystals in the engineering core.
- Seven large crystals in the weapons lab.