Rookie CIA analyst Alex O'Connor is assigned his first case - to examine the statements of a defecting Russian spy, who claims that rogue elements within her organization are planning a catastrophic attack that will bring America to its knees. Unbeknownst to Alex, his parents, Katya and Mark, are part of the dormant Russian sleeper cell he's investigating, and an unwelcome friend from the past arrives on their doorstep to give them a new mission: turn their son into a spy before his investigation unmasks them. With nowhere to turn, Katya and Mark must choose - flag, or family.
Mark and Katya are nearly exposed as spies by their own son, Alex. Then, in a brilliant bit of manipulation, Katya manages to convince Alex he is wrong. Katya's lies cause a rift between her and her husband and son. Victor is acutely warned of what will happen to him if he doesn't keep the O'Connors on a tight leash. Meanwhile, Alex partners with Agent Michelle Prado as part of a joint CIA-FBI task force to find the hidden SVR cache before it's destroyed. Alex's unique perspective is the key to unmasking the identity of a new defector, leading to a deadly confrontation with an SVR hit team.
In the aftermath of a violent shootout, Alex must convince the FBI to risk a dangerous covert operation to find Mikhail's hidden cache. With Agent Prado at his side, Alex leads a team to Philadelphia to retrieve the laptop from a secure government building, but Victor is a step ahead and orders the O'Connors to break in and steal the laptop first. Meanwhile, Katya discovers one of Natalie's most dangerous secrets, and forces her to choose between love and family.
Shocking discovery leaves Alex struggling to reconcile his theories with the evidence found at City Hall, and Sam encourages him to keep looking for clues. Meanwhile, Mark and Katya must answer for their actions when the Rezident doubts their commitment to the cause, and Natalie learns just how lethal Black Dagger will be if they don't stop it.
Alex is confronted with the reality of his family's past just as his integrity is questioned at work. The FBI suspects a mole in the organization and brings in Special Agent Faber to investigate. Faced with testifying under oath and submitting to a polygraph test, Alex must for the first time fight against his own moral standards. Meanwhile, Victor finds a new way to keep tabs on the O'Connors, and Natalie makes a critical mistake while tracking down a lead.
Michelle's shooting causes problems and turmoil for Alex, and his family try to help him. Meanwhile, Victor and Natalie want to push up their escape; and Oscar poses as a Boston native when he gets acquainted with his new New York City neighbor.