Pyramid Patrol is a very traditional FMV-based rail shooter. The player's ship and small enemies are sprites, while the stages are presented using full-screen FMV stored as laserdisc video. Pyramid Intruder, the 3DO port, improves on the original game by switching from a first-person perspective to a behind-the-ship view in order to make it possible to dodge enemies; it also adds new realtime 3D levels in between the original levels.

In the year 2035, humanity discovers a giant pyramid on the planet Mars. It turns out to have been created by the ancient people of Mu, whose advanced civilization had been forgotten by Earth, and who counterattack following humanity's intrusion.