Eine Grippeepidemie bedroht die USA. Innerhalb des Projekts NOAH wird an der Erforschung eines Virus' gearbeitet, das als Heilmittel für sämtliche Krankheiten dienen soll. Dazu wird ein Kind zu Versuchszwecken benötigt. Die Wahl fällt auf die zehnjährige Amy, die gerade Waise geworden ist. Als der in das Projekt involvierte FBI-Agent Brad Wolgast das Mädchen kennenlernt, ändert er jedoch seine Meinung und versucht, Amy um jeden Preis zu beschützen ...

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Amy und der verletzte Brad sind auf der Flucht vor Richards und seinen Männern. Als Brad bewusstlos wird, bittet Amy dessen Exfrau Lila um Hilfe aus der Ferne. Schließlich landen die beiden bei Brads ehemaliger Lehrerin Lacey in Wisconsin. Lacey organisiert die Flucht von Brad und Amy nach Kanada.

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Amy und Brad werden von Richards ins Forschungsinstitut gebracht. Dort wird dem Mädchen der Impfstoff gespritzt. Indes trifft Brad auf Carter, der im Zimmer neben Amy wohnt. Der erzählt von seinen Albträumen, in denen immer wieder Tim Fanning auftaucht.

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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. Meanwhile, the virals gain power over the facility's staff, leading Richards and Wolgast to reunite so they can take down a rogue soldier.

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With the sudden arrival of a high ranking official, Horace Guilder, to Project NOAH, Brad and Amy begin to strategize a possible escape plan with the help of an unlikely accomplice. Meanwhile, Sykes and Richards begin to question each other's motives, and 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.

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.

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.