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. When she discovers that she's pregnant with Vaughn's baby, she becomes determined to uncover the truth about him. Meanwhile, because of Jack's past betrayal by Irina, he begins to worry that his daughter may suffer the same fate that he did.
Sydney teams up with Renee - a fugitive on the CIA's most wanted list -- to track down the murderer of a close friend before the hugger can strike again. Meanwhile, Jack enlists a reluctant new agent, Thomas Grace, 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. Meanwhile, Dixon must accompany Sloane, who's given a 48-hour pass from prison to acquire a possible cure for his daughter, Nadia.
Sydney's life hangs in the balance when Gordon Dean discovers that Rachel -- aka Mockingbird -- is still alive. Meanwhile, Sloane awaits the outcome of his sentencing.
Sydney and Tom discover that Rene has stolen the cryogenic-type container, and they find themselves under siege by mercenaries who want the container's contents. Meanwhile, Sloane is forced to take matters into his own possibly devious hands to get himself reinstated into APO and to continue his quest to find a cure for daughter Nadia.
Sydney must guide a nervous and pensive Rachel on her first solo mission. Meanwhile, Sloane must decide whether or not to betray the trust he's recently earned with APO by honoring his agreement 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.
After Rachel has a fling that inadvertently compromises a mission, she and Sydney are forced to team with Julian Sark to prevent a deadly micropulse bomb from getting into the hands of a dangerous mercenary. Meanwhile, Jack and a former lover -- an MI-6 agent -- fight for their lives after being captured.
Sydney is reunited with Vaughn after being kidnapped and put in a hypnotic state in order to retrieve information from the depths of her mind. But unbeknownst to Sydney, her captor is a familiar face with a vested interest in Sydney's future and the future of her unborn child.
Jack calls on former Agent Weiss and the APO team to search for Sydney after receiving a distress call from her. But Jack believes that a larger conspiracy may be in play, thwarting their attempts to rescue her. Meanwhile, Tom's suspicious actions may suggest he has a hidden agenda, Irina Derevko is a surprise partner to Jack and a very pregnant Sydney on a mission to retrieve The Horizon but her allegiances still remain in question -- and Sloane is forced to scramble when Devlin suspects a mole is working inside APO.
Jack calls on former Agent Weiss and the APO team to search for Sydney after receiving a distress call from her. But Jack believes that a larger conspiracy may be in play, thwarting their attempts to rescue her. Meanwhile, Tom's suspicious actions may suggest he has a hidden agenda, Irina Derevko is a surprise partner to Jack and a very pregnant Sydney on a mission to retrieve The Horizon but her allegiances still remain in question - and Sloane is forced to scramble when Devlin suspects a mole is working inside APO.
Sydney's maternity leave is cut short when she learns that Will has been abducted by her nemesis, Anna Espinosa. Meanwhile, Sloane finds himself one step closer to obtaining the cure for daughter Nadia.
Sloane is distressed to learn that Prophet Five's cure for Nadia is just as likely to hug her. Meanwhile, the search for Anna Espinosa continues, Rambaldi's prophetic Page 47 resurfaces, and Sydney offers Rene a job at APO.
Sydney must beat arch-nemesis Anna Espinosa to the punch when a mysterious chip found implanted in Renee is tied to Vaughn. Meanwhile, Sloane struggles with ghostly visions while working for Prophet Five.
Syndey has to stay undercover while partnering with Sark to find Rambaldi's final clue before Prophet Five gets to it first. Meanwhile, Vaughn sees Isabelle for the first time and Tom's secret is revealed to Rachel.
Sloane takes Marshall and Rachel hostage in order to get information about Rambaldi's plan while Syndey and Vaughn race to stop him before it's too late.
Peyton tells Sloane that she has made a deal for the Rambaldi Sphere with an ally in China. Sloane arranges for stolen missiles to be sent to Hong Kong. Sloane's plan is revealed to the APO members, who race to stop him before he can use the Rambaldi Sphere to put the plan in motion. But this all leads to a long awaited confrontation between Sydney and Irina.