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 gets stranded in 2016 after an attempt to destroy the virus changes the future; Jones and Railly deal with the consequences of the changed timeline.

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.

In the present, Cassie and Jennifer Goines run from the 12 Monkeys; in 2044, Cole and Ramse face off against Deacon.

Cole and Ramse travel to 1970s New York City to prevent the Twelve from murdering a Vietnam veteran with a connection to the Witness.

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.

After the tragic events of the meltdown, Jones is left with the disheartening realization that humanity's true enemy is time-travel itself. As its architect, she elects to do the unthinkable - send Railly back in time to 2020, to kill Jones while she was still at Spearhead in order to undo all of it. However, Cole and Railly discover a shocking anomaly in their quest to carry out Jones's wishes

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. Written by sarahvilhelmsen

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.

As the temporal facility gets closer to destruction, Cole goes to 1957 to save humanity while everyone else looks for Titan, the stronghold of the Witness.

With time running out, Cole and Railly splinter back to 1957 in an attempt to find the last paradox Primary. With the machine destroyed, Ramsey, Deacon, Whitley, Jennifer AKA Mother and Hannah go across country in a last-ditch attempt to find Titan and kill The Witness. Written by Snowball

Cole and Railly adjust to the past, but a mysterious woman with apocalyptic visions gets them to do the unthinkable to save the world.