After Agent 5’s success in the previous games, time travel technology is deemed unsafe and the TSA is forced to close down.

When Agent 3, the culprit from Buried in Time, causes a temporal rip, Gage Blackwood must travel back in time to find her. He discovers that aliens had destroyed three ancient Earth civilizations.

After finding Agent 3, he learns that a mysterious alien fleet has appeared in Symbiotry space and is heading toward Earth in search of an ancient alien relic known as the Legacy of Time. Joined once again by his AI buddy Arthur, he must track down the pieces of the Legacy in Atlantis, Shangri La, and El Dorado.