In the near future, the military has created an advance computerized combat simulation, which allowed participants to be trained in various forms of combat throughout human history. However, a programmer working for a corporation that seeks the downfall of the simulation developers infects the system with a virus. This virus creates a dimensional vortex that threatens to swallow the entire world. Stanley Opar, a member of S.A.V.E (Special Action for Virus Elimination) enters the vortex with one goal: destroy the virus before the universe ceases to exist.

Time Commando is an action game with light puzzle-solving elements. The player character travels to eight different time periods: Prehistoric, Roman Empire, Feudal Japan, Medieval, Conquistador, Wild West, Modern Wars, and Future. Each era has its own characteristic enemies and sets of weapons: for example, Stanley fights with rocks and bone knives in the Prehistoric era, switching to shurikens and katanas in Japan, revolvers and shotguns in the Wild West, laser pistols in the future, etc.

Most of the time in the game is spent fighting enemies. Character navigation and combat resemble those of Alone in the Dark. The navigation is character- rather than camera-based, similarly to survival horror games. During combat, Stanley has three attack moves at his disposal, as well as a blocking move. Part of the challenge relies on choosing the right weapons against particular enemies.

Stanley starts with a small life bar that can be increased by picking up life power-ups, as well as multiple lives. Time limit is imposed on each level. To lower the countdown, the player has to deposit computer chips collected throughout the levels in special orb pools. The game utilizes animated pre-rendered sequences to represent locations, and polygonal models for the characters.