Cole is led to Haiti in 2014, where a dangerous outbreak proved to be a devastating moment in Dr. Railly's life.
Jones turns to Ramse for help getting Cole and Cassie back from 1944; Jones visits old Jennifer Goines to explore the true nature of time.
Jennifer Goines forms The Hyenas to take on the 12 Monkeys' organization, and with the help of Cole, they discover a plan to acquire the virus.
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.
Jones realizes that humanity's true enemy is time-travel itself, and decides to send Railly back to 2020 to undo everything; Cole and Railly discover an anomaly during their quest.