Season four begins with Annie swiftly ascending an elevator, racing upwards towards a mysterious – and no doubt dangerous – meeting. She makes an emotional call to Auggie, and, ignoring his pleas to come home, pulls out a gun. Then the elevator doors open, and all hell breaks loose…
Upon her return from Columbia, Annie gets a surprise visit from Arthur, disgraced following his recent revelation of infidelity and resignation from the CIA. Determined to protect his secret connection to terrorist Teo Braga—and most of all to protect Joan from being damaged by it—Arthur asks Annie and Auggie to keep what they know to themselves and help figure out Henry’s endgame.
Armed with a new file from Henry, Annie calls a secret meeting with Arthur and Joan to tell them what she’s learned: Teo and his terror group are planning to bomb an American target in Columbia. Arthur discloses the truth about Teo: that he’s a double agent who infiltrated the ALC to avenge his mother’s death.
As Annie and Auggie’s romance heats up, both begin to notice how it strains their working relationship within the CIA. Arthur and Henry almost come to blows.
With a new glamorous NOC in place, Annie is sent on an undercover op to Vienna, forcing her to cut off all communication with Auggie. Joan and Arthur determine that now is the time to bring in reinforcements.
Annie gets involved in an FBI investigation in order to cover her tracks. Elsewhere, Henry presents Annie with a major opportunity.
Annie finds she has met her match when she has to work to halt the illegal sale of deadly weapons and is teamed up with a seasoned operative; circumstances force Auggie to deal with past demons' Calder's suspiciouns of Annie Walker grow.
Annie asks Teo to betray one of his own in order to neutralize Henry; Calder's true colors emerge after Joan makes a shocking choice; and Auggie gets into trouble.
A stunning revelation catapults Annie to Copenhagen where she must stop Teo from committing a terrible act. Auggie discovers where Calder’s allegiances lie. Arthur enlists Bianca Manning, DC’s top defense lawyer, to help save the Campbell name.
Henry Wilcox’s dastardly plan has all come to a head: Teo is dead, Arthur is facing treason charges, Joan and Auggie are suspended from their jobs, and Annie is on the run in Europe. Things are looking dire, but no one is quite ready to give up just yet.
Annie begins her first deep cover operation completely on her own. Meanwhile, Auggie, Joan, Arthur and the rest of the CIA manage the fallout from Annie's "death" at Calder's hands.
Despite his misgivings, Auggie decides to work with Calder on an alternate method to destroy Henry. Joan confronts Auggie about this alliance.
Henry reaches out to his only ally within Langley, Calder. Joan reveals something during her deposition that puts a wedge between herself and Arthur. An old flame reveals she still holds a torch for Auggie.
Annie travels to New York after receiving new intelligence. Elsewhere, Arthur's court date looms nearer, and Joan finds a solid lead.
Annie, Auggie and Calder go on an unauthorized mission to Hong Kong in the hope of apprehending Henry's courier. Meanwhile, Joan and Arthur reveal a traitor who's been hiding in plain sight.
In the season finale of Covert Affairs, Calder wonders if Joan is the only person he can trust when he returns to the United States with good news. Elsewhere, Annie and Auggie continue their work to bring Henry to justice.