Emily si odpykává poslední dny její suspendace v FBI a zároveň se snaží vyrovnat s důsledky svých činů z posledních dvou sezón. Emily je extrémně ostražitá a nedůvěřivá k ostatním. Všude vidí nebezpečí a všechny pečlivě sleduje.

Po osudných událostech musí Emily závodit s časem, aby našla a zachránila Nicka, s pomocí svého tajemného informátora. Poté co ho vystopují, si Emily uvědomí, že existuje mnohem větší spiknutí a musí čelit možnosti, že by Nick mohl být mrtvý.

Disoriented and drugged into a paralytic state, Nick wakes up in a dark and confined location. Meanwhile, without a body as proof, Emily refuses to accept that Nick is dead and makes a deal to get him back, only to find that Dawkins has laid a trap and everyone is in danger.

Emily’s demand for the FBI to go after Nick is met with resistance, which leads her to set in motion a risky plan that puts her face-to-face with the one man who can lead her to Nick. Meanwhile somewhere in Europe, Nick is being drugged and psychologically tortured, revealing his buried guilt and his insecurities as an FBI agent, a husband, and as a father.

Nick continues to be tortured but finds an opportunity to try to escape from his captors. Cal and Emily head off to rescue Nick and become closer along the way. When they reach the mysterious location, they find evidence that links to Nick’s case back in Boston, but there’s no sign of Nick.

Emily makes a final attempt to trade the stolen files for Nick and demands proof that he is alive, unaware that Nick has escaped from his captors in a thrilling chase. Nick makes contact with the FBI, and Emily makes a bold decision to confront Cal about his past.

Emily and Nick devise a plan to infiltrate the refugee camp, and Cal poses as a Meridian guard in hopes of finding Armstrong and bringing him to justice. Meanwhile, Crown and Gunnarsen narrow in on Meridian’s mole and an unexpected visitor arrives at the farm.

Nick works to free the refugees and Cal finally confronts Armstrong. When Gunnarsen and Crown go to arrest Deputy Director Webb, they discover something deadly. Meanwhile, Emily tries to get to the bottom of Elliot’s operation and goes to extreme lengths to protect her family.

Emily and Nick are finally reunited with Flynn back in Boston, but the threat of Elliot’s bioweapon still looms large. Emily resorts to drastic measures and make a dangerous choice to ensure her family’s safety.