"Covert Affairs" centers on a young CIA operative, Annie Walker, mysteriously summoned to headquarters for duty as a field operative. While Annie believes she's been promoted for her exceptional linguistic skills, there may be something or someone from her past that her CIA bosses are really after. Auggie Anderson is a CIA military intelligence agent who was blinded while on assignment and is Annie's guide in this world of bureaucracy, excitement and intrigue.
Annie forges a professional relationship with Henry Wilcox while also adjusting to her new romance with Auggie. But when Annie and Auggie head to Columbia searching for a new person of interest: the Puma, the spy game gets serious.
After a bombshell revelation rocks the CIA, Annie and Auggie combine forces with Arthur in an attempt to bring Henry’s hidden agenda to light. Joan finds a personal moment to confide in Annie.
Annie returns to Colombia and must determine Teo Braga’s true allegiances in order to thwart a potential act of terrorism. Joan begins a round of interviews that could significantly alter her career trajectory within the CIA.
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.
Annie is sent to Vienna, and must cut all communication with Auggie. Meanwhile, Joan and Arthur decide 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. Meanwhile, circumstances force Auggie to deal with past demons' and Calder's suspicions of Annie Walker grow.
Annie convinces Teo to turn on one of his men, while Joan makes a decision. Elsewhere, Calder shows his true colors and Auggie faces trouble.
Annie must stop Teo from committing a terrible act. Elsewhere, Auggie discovers Calder's allegiances and Arthur seeks help in defending the Campbell name.
Annie makes a desperate attempt to take down Henry. Elsewhere, Calder and Annie finally face off.
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.
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.
Annie Walker is removed from CIA training and thrust into the inner sanctum of the Agency for what appears to be their need of her exceptional linguistic skills, but there may be something or someone from her past that her CIA bosses are really after.
New CIA agent Annie Walker is still forced to work on low-key cases until she is tipped off that a IRA cell operates in America.
Annie is tasked with getting close to Diego, a college student, in the hopes that his sister, Julia, will provide the CIA with intel on Victor Ponces, a corrupt Venezuelan government official. But when the CIA station agent looking into Ponces goes missing, Diego's trust in Annie means that she's going to have to finish the job.
After a "simple brush pass" goes sour, Annie is stranded and on the run in Zurich with Eyal, a Mossad agent who can't be trusted. Meanwhile, as Auggie works to bring Annie home safely, Arthur and Joan are busy trying to track a leak coming from within the CIA ... and Auggie is near the top of the list
In order to stop a weapons shipment, Annie asks a former operative for help and attracts Henry Wilcox's and her former lover Ben Mercer's attention.
Annie is tasked with investigating a potential national security leak originating from the Senate Intelligence Committee. Elsewhere, Auggie is assigned as a stateside handler for his old special ops unit, and Annie is worried that her brother-in-law, Michael, is cheating on Danielle.
When communication systems throughout D.C. are shut down by a hacker, Auggie is put in the field to obtain the code for the CIA. But his excitement to be doing field work is tempered when he learns that the hacker responsible is Natasha Petrova ... who happens to be his ex-girlfriend.
After Annie witnesses a suspicious purchase at an art auction, her follow-up brings a surprise visitor -- Ben Mercer -- back into her life.
An Iranian trade delegation member attending the WTO conference in Toronto escapes his handlers and contacts the CIA, hoping to parlay stolen intelligence into safe passage to the United States.
Annie needs to be recruited by smugglers; Arthur and Joan must bring Henry Wilcox back into the fold.
Annie is forced to confront her past when Ben Mercer walks into CIA Headquarters.
After tragedy shakes up the CIA, Annie and the rest of the DPD find themselves in an unfamiliar situation.
Annie and Auggie are brought together for a DPD assignment, sending them to Spain to acquire a computer virus that China also wants to obtain.
When a situation develops while Auggie is visiting Parker in Africa, Annie, Joan and Lena have to find a way to work together to bring him back safely.
Annie investigates a break-in at a high-tech company and reaches out to the FBI for help. But her plan is complicated by Simon's unexpected arrival in town.
When proprietary American technology is found in an Iranian missile, Annie is sent to Israel where, along with Eyal Lavin, she attempts to discover who leaked the technology.
When the Prime Minister of Yemen arrives in the US for emergency heart surgery, Annie takes on a near-impossible assignment: with a three-hour window, no back-up, and the State Department warning the CIA not to interfere, Annie attempts to turn the Prime Minister's Chief of Staff into a CIA asset.
When Simon invites Annie on a trip to Cuba, she accepts, knowing this is her best opportunity to learn what Simon has been planning. But going to Cuba means Annie won't have any backup if she gets caught.
After it's discovered that Jai was investigating Simon Fischer when he was killed, bringing Simon in becomes Arthur's top priority. In the hopes of protecting Simon, Annie requests that she be allowed to bring him in herself.
As the life of one the Agency’s best hangs in the balance, the team works to discover the truth after it’s revealed that one of their own might not be who they thought.
The CIA attempts to obtain proof that an enemy is hiding in Russia, in the hopes of bringing them to justice.
When Annie's mission in Russia goes awry, landing her in prison, Auggie, Joan, and Arthur work with an old friend to bring her home safely.
Things become complicated for Annie when Eyal Lavin and his boss, Rivka Singer, request the CIA's assistance tracking down a Mossad asset.
After receiving intel from Mossad warning that two suspected terrorists are planning to meet, Annie finds herself in a race against the clock to track down the meeting location before the targets get away.
When a crucial CIA asset disappears from protective custody, Annie and Eyal work to find her before they lose her forever.
With Auggie in Iraq and Joan out of the office, Annie turns to Eyal to help her track down Khalid Ansari.
When a fellow spy is taken hostage, Annie travels to Amsterdam to eliminate Khalid once and for all.
Annie and Auggie consider their future just as a connection from the past resurfaces and leads Annie on a race against time to prevent a terrorist attack on U.S. soil. Elsewhere, tension mounts between Calder and Joan as they wait to see who will become the new DCS and Arthur considers about a career in the private sector.
Annie thinks about working with Ryan McQuaid in an effort to catch a terrorist in Venezuela. Auggie is questioned by the NCTC.
After a botched escape attempt, Annie and McQuaid combine forces to get out of Venezuela. Joan works with Arthur and his new co-worker, Caitlyn Cook, to extract their fellow operatives. Calder’s clandestine affair takes on a new dimension.
Annie begins a stake out which ends less than routinely after the CIA discovers that a member of the intelligence community may have leaked confidential intel. Joan and Arthur both vie for a piece of government funding, as Calder’s personal and professional lives collide.
Auggie's emotional history with a potential asset complicates a mission when he and Annie switch roles as operative and handler in Paris. Joan attempts to play matchmaker for Calder. Arthur heads on his first operation abroad for McQuaid Security.
While on an undercover mission, Annie must keep her guard up after she accepts an invitation to the Russian Embassy in Paris. Auggie attempts to juggle more than one relationship, while Joan unravels the details of Arthur’s most recent business trip.
Annie and McQuaid travel to Azerbaijan in search of a mysterious, off the grid ex-CIA officer. Auggie’s devastated to discover unfortunate details about an old friend. Calder’s actions lead to a confrontation with Joan.
A reliable source spurs Annie and Auggie to dig deeper into a conspiracy theory that shed light on an attack on the CIA. Joan and Calder are forced to make a difficult decision.
Annie begins a sensitive undercover operation without the CIA’s support. Calder interrogates Auggie about a potential breach of protocol. McQuaid Security welcomes a new recruit.
Annie helps McQuaid accomplish a tough mission against Auggie’s wishes. As a threat on U.S. soil appears imminent, Hayley becomes more dogged in her pursuit of the truth.
McQuaid's health hangs in the balance; Annie seeks information in Istanbul; Arthur takes control.
Annie searches for a rogue chemist in Germany; questions about Joan's time in the Balkans.
After a startling revelation, Annie works with a new ally; McQuaid and Joan go into the field.
Annie and McQuaid must sneak into Russian territory in pursuit of Belenko.
Annie and McQuaid's relationship deepens while tracking down Belenko's next target.
With Russian Vega Force assassins on their trail, Annie and McQuaid work together to escape.
When Annie and Ben go back to Washington DC, Ben goes missing. Annie is assigned to keep a professional tennis player from Estonia safe.
Annie meets Mossad agent Eyal Lavin again when they both try to turn a secretary working at the Syrian embassy in Paris into an asset.
The leak of a CIA Trainee's name brings Annie back to The Farm with the sensitive task to find the culprit without being exposed herself which would end her own CIA career.
Annie runs into a set up when she tries to exchange a spy named Carlo Reni in Argentina. They escape the assassin and go on the run, trying to find the one responsible before the assassin can finish the job.
Annie looks into a potential leak at NASA, which could threaten the U.S.'s spy satellites. During the mission, she must also adjust to working with a new tech operative after Auggie moves to a new position.
Annie and Reva are captured near the Polish-Belarusian border by a man (Peter Stormare) working for the secret Soviet police when they try to deploy surveillence cameras in the Bialowieza Forest. Meanwhile Jai assembles an extraction team to rescue them in Belarus.
Auggie is aided by a flight attendant (Rebecca Mader) while on his vacation to the international jazz festival in Istanbul. His trip turns into a mission when he inadvertently records the voice of the man who injured him during the war in Afghanistan.
When a covert CIA operative and friend of Joan's gets caught up in a hostage crisis in Mexico, Annie and Joan are sent to assess the situation under the cover of being a news team. But when Arthur decides that they need additional backup, he sends Ben Mercer to assist them.
Annie learns that her college professor Mark Ramsay was secretly working for the CIA when he was killed tracking a Pakistani spy ring. The CIA asks Annie to find the missing intel using her connection to Ramsay's widow Safia.
While Annie runs the extraction of a Chinese scientist named Shen Yue who is willing to defect, she runs into complications and is forced to make a difficult choice.
Annie feels lonely during some downtime following a failed mission in Venice. Another assignment soon comes up, however, involving a chef tied to a Basque separatist movement.
While on the trail of Isaak Von Hagen, a known money launderer, Annie prepares to turn his wife, Elsa, into a CIA asset.
Annie is sent to find Mossad agent Eyal Lavin after it's discovered he's in Washington D.C. posing as a CIA operative.
Annie keeps tabs on the daughter of a CIA analyst imprisoned for selling intelligence. After an asset is killed in Russia, the CIA suspects the woman could be helping her father.
A MI6 operative asks Annie for access to the Smithsonian. Since he doesn't know that Annie's a CIA agent, she decides to cooperate in order to find out what he's after.
Annie and Danielle's vacation in Stockholm turns dangerous when Danielle is mistaken for a spy, putting her life in danger.