Um vírus mortal invadiu o computador ultrassecreto dos militares. Empurrado para um túnel do tempo mortal. Você deve lutar contra a história e o futuro, correndo contra o tempo para restaurar a memória do computador antes que um crescente vírus de computador se torne invencível. Prepare-se para a viagem no tempo mais brutal de todos os tempos.

Time Commando unfolds at the Historical Tactical Center, a military facility where a powerful computer has been built to simulate combat drawn from any era of human history. Disaster strikes when a programmer working for a rival corporation sabotages the system, unleashing a so-called Predator Virus that tears open a time-distortion vortex. Left unchecked, the growing anomaly threatens to consume the entire world. To avert catastrophe, the player takes control of Stanley Opar, an operative of S. A. V. E. , the facility's Special Action for Virus Elimination unit. Stanley plunges directly into the vortex to hunt down and destroy the virus at its source. His mission carries him through a succession of historical periods, from the prehistoric wilds and the Roman Empire to feudal Japan, the medieval age, the Wild West, and beyond, each demanding he fight for survival with the weapons of that era. Racing against time itself, Stanley battles ever deeper toward a final confrontation with the virus.