As an imminent flu epidemic threatens the U.S., Federal Agent Brad Wolgast is tasked with bringing in the experiment's latest chosen test subject, a ten-year-old girl, Amy Bellafonte. But, after meeting Amy, Brad's loyalties to Project NOAH are tested.

Amy and a wounded Brad continue on the run from Richards and attempt to seek refuge with an elusive, ex-military instructor of Brad's, while Lila tries to help from afar. Meanwhile, at Project NOAH, Dr. Lear reflects on the decisions that compelled him to involve Fanning in his research, and testing of the virus on Anthony Carter begins, as the epidemic in China spreads and the race for a cure intensifies.

Brad strikes a deal with Sykes and Richards to stay with Amy at Project NOAH, as they begin to test the virus on her. Upon learning the harsh truth regarding the state of inmates in 4B, Brad forms an alliance to get more information. Meanwhile, Babcock sheds light on her past.

When the only way to stop Fanning and the virals' escape from Project NOAH involves a dangerous explosion that could leave Brad, Sykes, and the cure for the virus caught in the crossfire, Amy must be the one to decide what's best for humanity. In the wake of this, surprising alliances form and a key figure returns to instill confidence, convincing everyone to fight for their lives.