Sydney returns to SD-6 and is assigned with Dixon to travel to Moscow to retrieve some stolen files. But when Sydney discovers that she has inadvertently given SD-6 access to a nuclear weapon, she is forced to travel to Cairo and face a deadly foe. Meanwhile, Will begins to question the circumstances surrounding Danny's death, and Sydney learns of her father's involvement in the murder.

Sydney's secret double agent status is jeopardized after she smuggling a biotech engineer into SD-6 from her mission in Berlin. Will meets a woman who confesses that she was having an affair with Danny shortly before his death. Vaughn informs Sydney that her father may be working for a third secret operative agency.

Sydney's life is placed in mortal danger when Sloane is informed by his superior that she is the SD-6 mole. Meanwhile, Dixon's life hangs in the balance after he is shot on a mission, and Will realizes that his discovery of Kate Jones' pin could uncover some unexpected information.

Vaughn asks Sydney to use her friendship with Sloane's wife, Emily, to gain access to a mysterious Rambaldi book which happens to be under lock and key in a safe at Sloane's home. Meanwhile, Will is kidnapped and told to drop his investigation of SD-6 or risk the lives of his family and friends, including Sydney's.

While the FBI detains and questions Sydney about her past and possible ties to a mysterious Rambaldi doomsday prophecy, Vaughn and Jack must race to free her and find a way to clear her name before her cover is blown and SD-6 is made aware of the situation. Once the rescue op has been launched, in her quest to prove her innocence, Sydney shocks even her usually unflappable father when she makes a chilling discovery that may unravel the mystery of the 500-year-old prophecy – she finds proof that Rambaldi's writings may hold more truth about an alleged weapon of mass destruction - and the fate of her own family.

Will's life is about to change as he is sent to find the person responsible for leaking information to him about SD-6. Meanwhile, Sloane finds himself on the cusp of finally tracking down Khasinau when SD-6 captures "The Man's" right-hand man, Mr. Sark. Dixon becomes suspicious of Sydney's activities.

Sydney finds herself face-to-face with her mother, whose intentions for her daughter are made chillingly clear. Meanwhile Sydney continues her search for Vaughn, not knowing if he is dead or alive after being swept away by a wall of water in Taipei. Will's life is forever changed when he learns the truth about SD-6 and Sydney's life as a double agent. Dixon must decide whether or not to inform Sloane of Sydney's suspicious activities.

Sydney discovers a terrifying secret when she's sent on a case to track down a new generation of weapons. Meanwhile, Vaughn suspects Jack of setting up Sydney's mother to take a fall. Sloane tells Jack the truth about Emily's death.

Sydney, Jack and Irina must put aside their differences and go undercover as a loving family in order to seize six nuclear warheads from an unfriendly nation. Meanwhile, Sloane announces to a suspicious staff that Mr. Sark will be working with SD-6, and later he is contacted by an unknown group claiming that Emily is still alive.

While continuing on a mission to take control of six nuclear warheads, Sydney and Jack discover where Irina's loyalties lie when she meets up with Gerard Cuvee. Meanwhile, Sloane informs the Alliance that Emily may still be alive.

Sydney, Vaughn and Jack must determine whether CIA agent Lennox is who he says he is after his deep cover mission is compromised.

Sydney begins to question where Vaughn's allegiances lie when she learns through CIA Agent Yeager that he is under investigation by the Agency. Meanwhile Irina and a crucial Rambaldi manuscript are used as bait to try to catch Sloane, and Sydney welcomes Dixon to the CIA.

Sydney begins to question Will's identity when he's arrested for espionage, under suspicion of being a double. Meanwhile Sark and Irina plot to recover the Rambaldi heart, and Sloane makes Jack a business proposal.

Sydney tries to piece together the last two years of her life and discovers the fates of her friends and family. She confronts Vaughn about his marriage and learns the shocking fates of Jack and Sloane. Meanwhile, she is granted temporary CIA clearance on a case that may help her regain her memory.

While Vaughn's life hangs in the balance, Lauren butts heads with Sydney after learning the part she played in his stabbing. Meanwhile, Sydney further questions Sloane's allegiances after he is kidnapped by Kazari Bomani, a kingpin in The Covenant; Jack's cover is jeopardized when he meets with Simon to dig up information on Sydney's missing two years; and Marshall is sent on his second mission with Sydney, posing as a high-stakes, southern gambler.

After making a shocking discovery in the desert, Sydney agrees to submit to an experimental procedure conducted by an eccentric doctor, designed to retrieve her lost memories. But while Jack and Vaughn look on, Sydney's mind proves surprisingly resistant to letting her remember her missing time -- and the process of recovering it could end up killing her. Meanwhile, Lauren makes a great sacrifice in order to make her alibi believable to Lindsey after breaking Sydney out of NSC custody, and Sloane finds himself boxed in by an unlikely enemy -- one who wants to see Sydney Bristow eliminated permanently

Jack contacts a mysterious woman with ties to Irina to help him free Sydney and Vaughn, who have been captured and face a North Korean firing squad. But Jack is faced with a curious conundrum when the woman tells him that she will not put the rescue plan in motion until he fulfills a favor - assassinate Sloane.

After finding out that Lauren is working for the Covenant, Vaughn is told to keep up the façade of a happy marriage in order to keep tabs on his wife's activities. But he's in for a shock when he uncovers the truth about Lauren's mother, Olivia. Meanwhile, Jack refuses to help exonerate Sloane of his crimes and put in motion a stay of execution, and a monk discloses the identity of the Rambaldi "Passenger" to Sydney.

Lauren stages a stunning betrayal to steal classified materials from the CIA. Meanwhile, Vaughn comes face to face with his darkest demons in pursuit of his wife; Nadia must decide whether or not she can trust her father, Sloane, in the pursuit of Rambaldi's most priceless artifact; and Sydney receives a shattering revelation that will make her question everything - and everyone - she thought she could trust.

Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn.

Sydney unwillingly teams up with her father to hunt down a modern-day samurai. Meanwhile, Nadia doesn't want to go back to the spy business, but is forced to when Sydney's life is jeopardized. Sydney finds out the reason behind Jack's misdeed and Nadia makes an unsettling promise.

Nadia puts her own life - as well Sydney's and Weiss's - in danger after failing to unveil her past through a dangerous criminal. Meanwhile, Vaughn finds a person who is somehow connected to his father and Nadia as well.

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.