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's loyalties are tested after a tragedy exposes the dark side of her superiors and the underhanded doings of her own father.

When armed intruders take over SD-6, led by McKenas Cole, a man bent on exacting revenge on ex-boss Sloane, Sydney and Jack must work together to save their colleagues. Meanwhile, Will fears that his investigation of SD-6 and its link to the murder of Eloise Kurtz is placing his life in jeopardy.

Vaughn disobeys orders and attempts to help Sydney and Jack avert the destruction of SD-6 headquarters and all its occupants. Meanwhile, McKenas Cole continues his vendetta against Sloane and searches for a mysterious device. A desperate but determined woman convince Will to continue his investigation of SD-6 and the imprisonment of David McNeil.

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 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.

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.

When a mission goes wrong, Sydney's is placed in danger and Marshall is the only one who can save her. Meanwhile, Dixon is exposed to a deadly pathogen released inside APO.

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.

Jack, Sydney, Irina, Vaughn and Nadia parachute into Sovogda. They're supposed to dismantle a giant red ball turning people into zombies. At APO, Marshall and Weiss use the Blackwell Index to blackmail the Russian minister into giving them the access codes to a Russian satellite, they discover that Elena is uplinking the satellite. A CIA agent, Brodien reminds them that the Rambaldi device is broadcasting a subaudible frequency that physiologically alters people who drink it and it is irreversible. Elena learns of the APO team's arrival.

Sydney gets shocking info on her dad's role in Danny's murder and takes on a countermission against the SD-6 to bring down an arms dealer linked to a missing nuclear weapon. Meanwhile, Will begins to grow suspicious of his friend's secret life; and Vaughn is taken off Syd's case after his mishap puts the entire world in danger.

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.

In order to catch Khasinau and get closer to finding her mother, Sydney and Vaughn set up an undercover transaction for a Rambaldi artifact with Khasinau's representative, Mr. Sark. But Sydney's cover may be compromised when a SD-6 agent is sent in to thwart the sale. Meanwhile, Will is enticed to continue his investigation of SD-6 when he learns the identity of one of his kidnappers. Emily tells Sydney that she knows about SD-6, which forces Sloane to make the most difficult decision of his life.

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.

After completing his first mission with Sydney, Marshall's life is placed in mortal danger. Meanwhile, Ariana Kane suspects Jack as being the prime suspect in the disappearance of Sloane's wife. Vaughn learns the truth about Jack's involvement in the murder of CIA agent Haladki and Sydney confides in Francie about her feelings for a fellow co-worker.

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 and Dixon go on a dangerous case involving the safety of the United Commerce Organization. Francie confronts Charlie about his secret date with another woman, and Will continues to get closer to the truth about Danny's murder.

While helping Shepard escape from the asylum in Bucharest, Sydney discovers the shocking connection he has with her past. Meanwhile, after tracking the computer virus secretly planted by the CIA, Sloane is confronted by Alliance representative Alain Christophe, who suggests that one or more moles may have infiltrated SD-6. Will continues to investigate the woman claiming to be Danny's mistress and Sydney finds out the truth about her father's involvement in her mother's death 20 years earlier.

Sydney must undergo an extensive lie detector test to satisfy Sloane's frantic search for the SD-6 mole. Meanwhile, with nemesis Anna Espinosa following her every move, Sydney seeks out the connection that a device may have to the 500-year-old prophetic Rambaldi sketch. The mystery of Kate Jones deepens as Will continues to investigate Danny's death; and Sydney discovers that a keepsake from her mother Laura contains more disturbing connections into Jack's past alliances.

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 tested by the DSR to discover her mysterious link to a chilling 500-year-old picture and prophecy foretold in a Rambaldi manuscript. Meanwhile, after uncovering the identity of the rogue group leader, "The Man," Sloane learns through fellow Alliance of Twelve member Edward Poole that a close friend may be in cahoots with the enemy.

Sloane begins to question where Noah's true allegiances lie, as passion ignites between Sydney and Noah. Meanwhile, Sydney continues to uncover new information about her mother, which disturbes Jack. A rogue assassin known as the Snowman is dispatched by K-Directorate to kill Khasinau, a.k.a. "The Man." Will and Francie confront Sydney about the mysterious airline ticket stub found in her jacket.

Sydney finally learns the shocking truth about her missing two years from an unlikely source.

Sydney and Vaughn go undercover as a married couple so as to find a weapon that could bring back the Dark Ages. However, the neighborhood they've infiltrated is not as charming as it seems.