Cole and Dr. Railly face off with the Army of the 12 Monkeys when both discover the Night Room –- an off-site, black ops lab that houses the virus that will one day destroy the world.

With Cole dying from the effects of time-travel, Railly must find the one person who can save him.

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 faces the Witness as Cassie's hallucinations evolve; deadly visitors from the past arrive when the time machine malfunctions and begins tearing apart time and space.