The director of the project, Dr. Aiden Krone, rigs the laboratory to explode, takes the Alpha Suit and travels into the past.

Once there, he uses his knowledge to alter the timeline, placing himself as the ruler of the Krone Magistrate that controls a dystopian world.

The protagonist travels through the battle-torn city and witnesses the rebel forces being violently suppressed by Krone's army.

During the transport, however, parts of the Beta suit are damaged, rendering the protagonist unable to revert to the original timeline.

The protagonist is forced to assist the Occupant Rebellion against Dr. Krone in hopes of salvaging parts from the Alpha suit.

He meets Commander Cooke, leader of the Occupants, and is tasked with carrying out several operations, including rescuing POWs and destroying Krone's munitions plant.

The protagonist returns to Alpha District in an altered version of when he first arrived, only this time the rebels are dominating the battle.

As an incapacitated Krone emerges from the wreckage, the protagonist executes him and retrieves the part required to repair the Beta suit.

Short flashback sequences are shown at various parts throughout the game, which reveal that the protagonist was in contact with an unknown third party, was keeping watch on Dr. Krone in case he goes rogue, and has seduced Dr. Foster specifically to get access to the Beta Suit.

However, on April 10, 2007, Vivendi Games announced that they were giving TimeShift a complete overhaul and were fixing many bugs.

After the retooling of the game, Saber introduced "the suit" as the time control device, making the protagonist anonymous.