Former CIA agent Erica Shepherd, now known as one of the most notorious traitors in recent American history. Shepherd is brought out of a federal Supermax prison by FBI Agent Will Keaton to help stop some of the most dangerous acts of espionage threatening the United States today.

Following the discovery that a U.S. ambassador is selling classified intelligence to a Colombian cartel, Shepherd devises a plan to catch him that will push Keaton's moral code to the brink. Keaton brings a new member onto the team.

When intelligence obtained by Shepherd during her stint at the notorious ADMAX prison is linked to a pending attack on U.S. soil, Keaton and the CoIntel team embark on a manhunt to find and stop a deadly international operative.

Once Shepherd convinces Keaton that Anna Cruz is a mole inside the FBI working for Tal, Keaton decides to keep his enemies close. With a fox in their henhouse, Keaton and the team spy on one of their own, hoping Cruz will lead them to Tal.

After a bomb explodes in Jersey City, the Cointel team captures a key planner, Sam Fathi, who can lead them to Tal, the mastermind behind the bombing. When Sam proves difficult to break, Shepherd convinces Keaton to detain a former Egyptian intelligence officer to help, leading to an urgent mission to stop another bomb from going off.

When the FBI intercepts stolen NSA software intended for Tal, Keaton uses the technology as an opportunity to go on the offensive and sends Shepherd undercover. Keaton must choose between catching Tal or saving the life of an innocent teenager.

Flashbacks to the past reveal the fateful events that led CIA Deputy Director Erica Shepherd to betray her country and the ensuing investigation that put her on a collision course with Will Keaton.

After a major Tal operative escapes CIA custody, Shepherd returns to Langley to help track the fugitive down. Shepherd and Keaton discover the CIA is withholding vital information on Tal, so they spy on the CIA to find out what the agency knows.

When a group of contractors working for the CIA is murdered, Keaton and the team discover the CIA is keeping secrets from the FBI regarding Tal. Shepherd's ex-husband finds out that Hannah has been lying and visiting Shepherd.

When a highly sophisticated Tal operative evades FBI custody and flees to the Swiss embassy, the Cointel team must go under cover. What begins as a smooth counterintelligence operation quickly devolves into a tense hostage situation.

Keaton and his team are able to intervene and stop the assassination of a high-profile congresswoman; Shepherd interrogates the congresswoman, who had previously used Shepherd's treason conviction as a launching pad for her political career.

Tal's war on the CIA expands to two fronts; Keaton and the CoIntel team must locate the domestic target before Chigorin launches an all-out assault on the unsuspecting innocents; Shepherd convinces Keaton to let her go to Cuba to thwart Tal's attack.

When a former CIA operative is murdered, Keaton enlists Shepherd to help recover valuable intel that could take down Tal once and for all. But the question remains, can Shepherd be trusted?