Despite 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 causes a temporal rip, Gage Blackwood must travel back in time to find her.

During his search, he discovers that aliens 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.

With his AI buddy Arthur, he must track down pieces of the Legacy of Time, an ancient alien relic, in the mythical cities of Atlantis, Shangri La, and El Dorado.