Gage Blackwood (once again controlled by the player) is visited by himself from ten years in the future as the plot begins in the year 2318, six months after the events of the original game. Someone has falsely accused the future Gage of tampering with historical relics, and it is up to the past Gage to travel back in time and gather evidence to clear his name.
Meanwhile, the Symbiotry of Peaceful Beings is debating Earth's monopoly on time travel technology, and this latest trial threatens to shut down the Temporal Security Agency (TSA). Gage visits locales such as Leonardo da Vinci's studio, the end of the Siege of Chateau Gaillard, and the Mayan temple of Chichen Itza after teaming up with an artificial intelligence entity named Arthur, and eventually finds the culprit, Michelle Visard, who is another TSA agent.
Gage is kidnapped by her and taken to an abandoned missile silo, where Arthur sacrifices himself to force Michelle to travel back in time, allowing Gage to finish his quest. Gage later discovers that another extraterrestrial race, the Krynn, is behind the crimes and framing of Gage for their own gain. Gage is able to stop the Krynn and save his future self, but his mind is erased and he is returned to his own time.