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 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.

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."

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.

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.

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

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.

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.

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.

Rambaldi's catastrophic endgame begins to fall into place as a giant version of the Circumference/Mueller device is found floating over city in Russia, driving the citizens made. After a wounded Dixon reveals that Irina is alive, Sydney, Nadia, and Jack set off to find her. Irina had been captured, and then duplicated using Project Helix, in order to give the impression that she was dead. Sydney and Nadia discover Irina is being held inside a camp in Tikal, safely in the clutches of Elena's army. Irina had apparently been working to counter Elena's organization, the Covenant, and actually PREVENT the Rambaldi endgame. Irina tells of a page she destroyed, a page that was key to Rambaldi's endgame. Under torture, she finally broke and recreated it for Elena. After a short respite, the transport turns towards Russia, and Sydney, Vaughn, Jack, Nadia, and Irina parachute down, towards Elena, Sloane, the Circumference....and destiny.

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.

Jack's illness has caused him to hallucinate about a cure. Sydney must recreate the time when Jack was working for the CIA and hid the only man who might be able to help him now. For this, Sydney must play her own mother. Meanwhile, Sophia moves in with Sydney and Nadia.

Sydney must decide whether her mother's goodwill gesture was sincere or an attempt to kill her. Will witnesses Francie discussing her restaurant plans with a man whose affiliations are questionable, and Sloane is made a full partner in the malevolent Alliance of Twelve.

Jack meets Alliance counterintelligence head Ariana Kane, who is sent in to investigate Emily's disappearance and to discover who is trying to blackmail Sloane. Meanwhile, Marshall is sent on his first mission with Sydney as his partner. Vaughn schedules Will to take a CIA psych test. Francie gets suspicious over Sydney and Will's secretive behavior.

While Alliance counterintelligence head Ariana Kane tracks Sydney in order to catch her fugitive father, Jack elicits Irina's help in finding Sloane's blackmailer. Meanwhile, Sydney and Vaughn risk exposing their covers to SD-6 when they share a romantic dinner together while on a case in France.

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 faces off with her mother, while Emily must decide whether to side with her husband or betray him.

Sydney defies her father in her attempt to rescue a kidnapped scientist, while Sloane, seeking revenge, becomes more dangerous than ever. Meanwhile, Francie manipulates an unsuspecting Will for his agency connections.