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Picking up from Season 2's cliffhanger, Bob Lee Swagger is taken hostage by Solotov, the world's greatest assassin. Julie and Isaac team up to help bring him home safely. Nadine confronts Senator Hayes about his connection to Atlas. A surprising piece of information about Bob Lee's own father sets off a whole new mission, while back in D.C., a mysterious operative begins plotting an attack.

Bob Lee visits a local prison for answers about his father Earl Swagger's murder in 1988. Julie takes a job helping Sam, the Swagger family's lawyer. Following their attempt to destroy Atlas, Nadine and Isaac scoop up her ex-boyfriend Harris Downey, who knows more about the rogue operation than he realizes.

Bob Lee's investigation into Earl's murder leads him to the local slaughterhouse; Nadine and Isaac's quest to take down Atlas forces them into an uneasy alliance with a former Atlas agent.

Armed with new details, Bob Lee hunts for the men responsible for Earl's murder; Julie follows a lead of her own; when Harris gets grabbed, Bob Lee joins Nadine and Isaac on a rescue mission.

Bob Lee visits a friend of Earl's to ask about a rogue operation in Vietnam; he joins his team to crash an event in D.C., where they cross paths with an operative on a mission of his own.

Bob Lee and Isaac are put through the wringer by a member of Earl's Vietnam unit; Julie stands up to the Bama family; Nadine sneaks into a high-tech security facility.

Closing in on the mystery of his father's assassination and its connection to Washington's power brokers, Bob Lee and Isaac track down a former "dark lord" of the Pentagon - now residing in a psychiatric hospital. Nadine is sent on a dangerous mission by a DOJ Agent.

An attempt on Sam Vincent's life leads Bob Lee and Julie to a stockpile of information left behind by Earl Swagger, which may have been the cause of his murder. Nadine, Isaac, Harris and Carlita take a run at one of the heads of Atlas.

Bob Lee drifts further apart from Julie as his search for Red Bama's son leads him to a fringe group known as The Alpha Boys. In hopes of getting more information regarding a possible attack on Washington, Isaac and Nadine use Earl's cache of information to schedule a meet with the President's Chief of Staff. Carlita betrays the group and disappears.

Bob Lee and Isaac's search for Carlita and the missing key card leads them to an off-the-grid Atlas training facility, where they're forced to confront their pasts. Nadine and Harris scheme their way into a face-to-face with a critical player in Atlas' plot to retain power. Julie's paranoia grows as she confronts the fact that Bob Lee is always putting their family in harm's way.

Reeling from new information regarding his father's death, Bob Lee uses Harris to help him get payback - putting them both in danger. Nadine and Isaac attempt to convert Atlas recruits to their cause. Julie experiments with putting life with Bob Lee in the rearview. Atlas moves forward with its ultimate plan.

As Bob Lee finds himself torn between his thirst for justice and keeping his family together, Atlas pivots towards a new gameplan, which will only expedite their mission. While Harris forges a relationship with a powerful ally, Isaac and Nadine investigate a clue gathered from Isaac's showdown with Jack Long.

Following the blast in D.C., Bob Lee attempts to put an end to Atlas once and for all, all while trying to salvage his marriage and tie up the remaining threads from his past. Isaac, Nadine, and Harris find new roles for themselves in the government.