Sydney Bristow discovers that her job as an agent for SD-6, a top-secret division of the CIA, holds some deadly secrets that threaten the security of the free world. In spite of being warned against it, Sydney reveals her secret to her fiancé, Danny, who later on is murdered. Sydney finds that her father, Jack, is also SD-6 and that the group is not part of the CIA, but actually an enemy of the United States. Sydney seeks the aid of the real CIA and is enlisted as a double agent under the command of operations officer Vaughn. Her mission now is to complete her cases at SD-6 while reporting her findings back to the CIA. But when Sydney finds out that her father is also affiliated with the CIA, she begins to question where his true allegiances really lie.

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 briefs her CIA handler, Agent Vaughn, on her recent captivity at SD-6 and is surprised when he unexpectedly gives her a Christmas gift. Meanwhile Jack has to find a way to save Sydney when he discovers that Sloane has ordered her tortured and killed for being the suspected SD-6 mole. Will may be making the mistake of his life when he begins to research a name heard on a mysterious audiocassette -- SD-6.

Sydney is grateful and proud of her father after he saves her life while on a case in Havana. But her admiration is short lived when Vaughn discovers further evidence that Jack may have been responsible for the deaths of over a dozen CIA officers many years earlier.

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.

In order to save Will's life, Sydney and Vaughn must destroy a familiar looking Rambaldi device, while Jack makes a risky deal with Khasinau's representative, Mr. Sark. Meanwhile, the CIA believes that one of their own is a mole for "The Man"; the Alliance comes to a decision regarding the fate of Emily Sloane; Dixon's suspicions about Sydney intensify; and Sydney finds herself face-to-face with "The Man."

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 and Jack are confronted by the new director of SD-6 who replaces Sloane, whose whereabouts and intentions are unknown. Meanwhile, romantic sparks begin to fly between Francie and Will.

Sydney finally confronts her mother, who reveals her true motivation. Sloane, for his part, begins to execute his new grand plan and Will struggles to figure out who's behind his set-up.

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.

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.

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.