Despite Agent 5's success in the previous games, time travel technology is deemed unsafe and the TSA is forced to close down. However, Agent 3, the culprit from Buried in Time causes a temporal rip and Gage Blackwood must travel back in time to find her, and 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 towards Earth, looking for an ancient alien relic known as the Legacy of Time. Joining once again with his AI buddy Arthur, he must track down the pieces of the Legacy in the mythical cities of Atlantis, Shangri La, and El Dorado.