Season two starts where the first one left off, with Annie and Ben escaping danger together again. This time, they barely survive an ambush at a hospital in Guam. Ben continues to be a magnet for trouble. Later, when Jai visits them at a safe facility in the States, we see there is no love lost between the two men.
Annie returns home and finds out that her sister's garage was burglarized. To make sure she hasn't "brought her work home," Annie and Auggie arrange for a team to enter the house and scan it for any clues that might mean a breach of security.
Meanwhile, Annie is tasked to bring down an Estonian mobster named Morozov. He's connected to Russian arms dealers and murders. The CIA has been receiving intelligence about Morozov through his mistress, a pro tennis player named Nadia. But when Annie approaches Nadia for more information, she makes it known that she no longer wants to work with the CIA.
Annie won't take "no" for an answer because she suspects that Nadia may be in danger. When she goes over Joan's head to approach Nadia, after being pulled off the assignment, Annie nearly exposes both herself and Nadia. To make matters worse, Ben has disappeared from the hospital he was moved to and now Annie has a big mess to clean up.