After learning that the man she has known as Michael Vaughn is under investigation and suspected of being a double agent, Sydney begins to question whether their business and personal relationship over the years had all been a lie.

Sydney teams up with Renée - a fugitive on the CIA's most wanted list -- to track down the murderer of a close friend before the killer can strike again. Meanwhile, Jack enlists a reluctant new agent, Thomas Grace (Balthazar Getty), and Weiss struggles to decide whether or not to accept a promotion that would force him to leave his colleagues.

Sydney is forced to partner on a mission with new APO agent Thomas Grace. They discover that Rachel Gibson -- a spy suspected of being involved in activities against the U.S. -- has something shockingly in common with Sydney.

While Sloane awaits the outcome of his sentencing, Sydney's life is put in grave danger when Gordon Dean discovers that Rachel is still alive.

Sydney and Tom discover that Renie has stolen the cryo container, and soon find themselves under siege by a group of mercanaries who want the contents of the container. Meanwhile, Sloane takes matters into his own hands to get himself back into APO.

Rachel receives a little help from Syd for her first solo mission while Sloan is back at APO in frequent contact with Gordon Dean.

Sydney and APO attempt to discover whom Gordon Dean is working for and what their end game is. Meanwhile, when the group claiming to have a cure for daughter Nadia continues to play mind games with him, Sloane struggles for control.

Rachel and Sydney have to join forces with Julian Sark to prevent a deadly micropulse bomb from falling in the hands of a dangerous mercenary.

Sydney teams up with Vaughn after being kidnapped and being placed in a hypnotic. What Sydney doesn't know is that the kidnapper is a very familiar face with an obscure interest in her unborn child.

The entire APO gang is trapped inside the CIA offices and Weiss saves them. However, Weiss will not be returning to APO, he will just be helping the others on a mission to obtain information regarding Sydney.

Sydney gives birth to the baby, but Sloane may need something from the newborn. Nadia awakens.

While the gang starts to learn more about the Prophet 5, Sloane is distressed to learn that Prophet Five's cure for Nadia is just as likely to kill her. Meanwhile, Devlin returns, the search for Anna Espinosa continues, Rambaldi's prophetic Page 47 resurfaces, and Sydney offers Renée a job at APO.