Despite the growing tension between them, Cole and Cassie time travel to New York during World War II to track down a dangerous member of the Twelve.

When Cole and Cassie are stranded in 1944, Jones must turn to the person she trusts the least to bring them home -- Ramse. For Ramse, this mission will give him a chance to atone for his sins -- but can he mend the broken relations between Cole and Railly? Meanwhile, Jones visits Old Jennifer Goines to explore the true nature of Time - and the Twelve’s method to destroy it.

Cole has his loyalty tested when Ramse and Railly go rogue, embarking on an unsanctioned mission that sends them to 1961 East Berlin. Once there, they have murder on their minds as they search for an unscrupulous German doctor who knows the location of "The Witness."

In 1953, Cole and Railly reunite with Agent Gale at the birth of the Army of the 12 Monkeys.

A clue to breaking the cycle leads Cole and Cassie to the 1960s. Christopher Lloyd returns as Zalmon Shaw, a devoted follower of the Witness.