As the story begins in the year 2318, six months after the first game, Gage Blackwood (once again controlled by the player) is visited by himself from ten years in the future. Someone has framed the future Gage for tampering with historical artifacts, and it is up to the past Gage to visit the past and find evidence to clear his name.
Meanwhile, the Symbiotry of Peaceful Beings is deliberating on Earth’s monopoly on time travel technology, and this latest trial threatens to close down the Temporal Security Agency (TSA). After joining up with an AI named Arthur, Gage visits locations such as the workshop of Leonardo da Vinci, the ending of the Siege of Chateau Gaillard, and the Mayan temple of Chichen Itza and eventually find the culprit, Michelle Visard, who is another TSA agent.
Gage is kidnapped by her and taken to an old missile silo, where Arthur sacrifices himself to force Michelle to jump to another time and allow Gage to continue his mission. Gage eventually uncovers that another alien race, the Krynn, is behind the crimes and the framing of Gage to further their interests.