Lucy, Wyatt, and Rufus follow Flynn into the past once again to attempt to prevent whatever act of changing history he's about to commit, but this time, he's not exactly changing history.
He sets his sights on Judith Campbell, a famous mistress, that has connections with many high-level men, including President JFK.
It's exactly these connections that he seeks to exploit to get his hands on a core to an atomic bomb, though why has yet to be revealed.
Lucy, Wyatt, and Rufus get so close to saving the day and preventing Flynn from getting the nuke, but Rufus is easily tricked by his old co-worker, Anthony, the man Flynn "kidnapped" to pilot his time-traveling ship. Only he wasn't kidnapped. For some reason, he is willingly putting aside his distaste for Flynn's consequences to help with the mission and alter whatever they deem is necessary.
Rufus also steps in front of Wyatt's gun when he has the opportunity to take out Anthony; therefore, the ship would be useless because they'd have no one to pilot.
Wyatt sends a telegram from the 1960's to 2012 for his late wife to receive to potentially save her, but it fails. And Lucy temporarily breaks things off with her new, spontaneous fiance, and moves back home with her mother.