Cole and Ramse mend their broken friendship while on the run from the Army of the 12 Monkeys. And in the year 2043, Railly and Jones navigate an uncertain future as Deacon and the Twelve command the Temporal Facility.
Cole comes face to face with the Witness, the phantom behind the Army of the 12 Monkeys as Cassie's (Amanda Schull) hallucinations undergo a chilling evolution. Making matters worse, the Temporal Facility becomes increasingly dangerous after the malfunctioning time machine begins to tear apart time and space, bringing back deadly visitors from the past.
In 2016 Jennifer is taking matters into her own hands, going after the tall man when Cole splinters back to help her. Cassie and Ramses are both looking for revenge, looking for a place called Titan and Katarina is trying to make sense of a newfound relationship.
Cole's loyalty is tested when Ramse and Railly go rogue and embark on an unsanctioned mission into 1961 East Berlin in the hopes of finding an unscrupulous German doctor who knows the location of The Witness so they can kill him.