Scientists from the near-future have begun work on creating a viable time machine. The project results in the creation of two devices, the Alpha Suit, a less advanced prototype jump suit, and the Beta Suit, a more advanced, so-called military grade model with features the Alpha Suit lacks such as combat-related timeshifting abilities and an integrated AI designed to prevent the creation of Paradoxes.

The director of the project, Doctor Aiden Krone, takes the Alpha Suit and travels into the past. Once there he alters the timeline, placing himself as the ruler of the Krone Magistrate that controls a dystopic world.

The protagonist, a fellow scientist whose name is never spoken (never mentioned in-game or in manual), then takes the Beta Suit and follows Dr. Krone back to the year 1939 (in an alternate timestream) to a place called Alpha District. He then proceeds to assist the Occupant Rebellion against Dr. Krone.