Project NOAH is a a secret medical facility, where scientists are experimenting with a dangerous virus that could lead to the cure for all disease, but also carries the potential to wipe out the human race. When a young girl, Amy Bellafonte, is chosen to be a test subject, Federal Agent Brad Wolgast is the man who is tasked with bringing her to Project NOAH. Ultimately, however, Wolgast becomes her surrogate father, trying to protect her at any cost.
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—ten-year-old Amy Bellafonte. 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. Dr. Lear reflects on the decisions that compelled him to involve Fanning in his research. 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. Babcock sheds light on her past.
In an attempt to protect Amy, Wolgast convinces Sykes and Lear to let them outside of the facility for exercise. As emotional flashbacks reveal Carter's life leading up to his death-row sentencing, Fanning's hold on those kept inside Project Noah grows stronger. The virals gain power over the facility's staff, leading Richards and Wolgast to reunite so they can take down a rogue soldier.
With the sudden arrival of a high ranking official to Project NOAH, Brad and Amy begin to strategize a possible escape plan with the help of an unlikely accomplice. Sykes and Richards begin to question each other's motives. A shaky past between Lear, Elizabeth and Fanning is revealed.
Tensions are high with a viral on the loose outside Project NOAH, as Guilder and Richards hurry to mobilize a search party. Amy volunteers to help in an unexpected way, causing friction between her and Brad. Lear tries to help a lucid Elizabeth understand the tough decisions he's made while at NOAH. A surprising connection between Sykes and Babcock is revealed.
Brad and Lila flash back through their history together as they plan to save Amy. The Secretary of Defense gives Horace Guilder full authority over Project NOAH, leaving Sykes and Richards terrified for what his plan of attack might entail. Meanwhile, the bond between Amy and Carter is stronger than ever, as he prepares her for Fanning's grand plan, and Lear fights to help Elizabeth before it's too late.
As Amy experiences symptoms of the virus that indicate she is close to turning, Brad brings everyone together, and Lila and Sykes race to perfect an anti-viral medicine to save her from Fanning. Meanwhile, Richards tries to keep Project NOAH contained when Guilder makes a mysterious decision to let go of most of the staff while also trying to ward off Babcock's attempts to get in his head.
Amy must decide what's best for humanity when the only way to stop Fanning and the virals from escaping Project NOAH involves an explosion that could leave Brad, Sykes, and the cure for the virus in the crossfire.