In season two, Annie's personal and professional lives crash into one another, and the balance of her relationships are forever changed.
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.