The search for Marshall is on while he is held captive and tortured by "Suit and Glasses," making him agree to rewrite the Echelon code. Sydney and Dixon retrieve damaged Echelon data from Vietnam where it was routed by Marshall before capture but her countermission for the CIA is foiled and SD-6 gets all the information they need to access Echelon.
During a visit to the CIA shrink, Sydney recounts her escape from her mother who shot her, her rescue of Vaughn who is nearly dissected, and Jack's diffusal of Dixon's suspicions about Sydney. She also comes to an understanding with Will who must destroy his career and credibility to save his life and SD-6's secret. Sydney's mother ends up turning herself in but her motives remain unknown.
Sydney must deal with conflicting emotions as her mother is hauled into custody of the CIA while Jack implores them not to trust anything she says. Sloane, unaware of Irina's captivity but aware of her dissapearance, orders Sydney to obtain a disk containing compromising information to the Alliance.
Sark has taken control of Irina's operations and Syd must go on a mission to hack into a camera system that can see through solid matter before it is launched into space.
Jack's concern for Sydney's relationship with her mother takes a turn and he makes special arrangements to protect her during a mission Irina directs her to revealing Irina's true colors in the process. Also, Sloan is haunted by evidence that his dead wife may be alive and sends Dixon to investigate while Will is tested by SD-6 by an undercover agent sent by Sloane.
On a mission to find a batch of "next generation" weapons in Russia, Sydney discovers that the weapons involve brainwashing children to become spies and the sickening truth that her father may have used the same technique on her when she was young. Also, Vaughn discovers the extent of Jack's involvement in their Madagascar mission and how he planted the explosives to set up Irina and ruin her relationship with Sydney.
Sydney works to free her mother when Jack's deception leads to Irina's sentencing to death. Jack attempts to explain his side and eventually makes a great sacrifice to regain Sydney's trust.
Sydney attempts to save Vaughn from Sark's virus by stealing the antidote but the mission is botched and she is captured. She makes a deal with Sark to deliver Sloane into his hands, though doing so means Sloane's death, in exchange for her life and the antidote.
With Sark having turned himself into SD-6, Sydney questions whether he can be trusted with her double agent status on the line as she and Dixon are sent to obtain nuclear weapon codes from Uzbekistan.
Sydney, Jack and Irina continue their mission to obtain the warheads. They manage to fend off an ambush but are racing against the clock because the Indians are preparing an airstrike.
Sark is nearly tortured at Sloane's hands for his apparent betrayal but Sark suggests it is someone else in SD-6. Sark is teamed with Sydney to retrieve a high-tech spy computer called Echelon from Cuvee which is Syd erases, as per the CIA counter mission.
Jack is ambushed during a meeting as Ariana Kane has made him the prime suspect as Emily's kidnapper and Sloane's blackmailer. Sydney begins to come under Kane's suspicions as well though Sloane can't accept it.
SD-6 gets a new director named Geiger to replace the Sloane. Sark tells Sydney thats Geiger accessed a secret network of Sloane's that may hold evidence to the Alliance.
CIA agent Jim Lennox appears to be a double agent as, under orders from Sloane, he kills Wallace, his partner and fiancee, before she can expose him. The CIA is unaware of Lennox's status and Sydney and Vaughn are sent to retrieve him from the laboratory of Dr.
Sydney announces her intentions to quit the CIA but is met with resistance from Kendall who threatens to ban her from visiting her mother. A mathematician named Caplan, his wife and son are kidnapped by Sark and Sloane, to force him to decipher Rambaldi documents and build a weapon for Sloane.
Sloane abducts Sydney but Vaughn manages to turn the tables to help free her before she gets too far. When Sloane partners with an Afghani terrorist, Sydney and Vaughn attempt to find a way in and Dixon holds key information that he won't give up.
Sydney is informed of unauthorized meetings Vaughn has taken with KGB and she becomes suspicious of him after he is put under investigation. She confronts him and he reveals he has been investigating Irina on his own time for his peace of mind.
Sydney is determined to get her mother. Meanwhile, Emily Sloane has to choose between standing by her husband or betraying him.
Syd rescues Dr. Neil Caplan with the help of his wife, a Russian operative who has betrayed her orders because she's fallen in love with Caplan. Meanwhile, Sloane seeks revenge against Dixon, who he holds responsible for his Emily's death and kills Diane in a car bomb explosion.
A Rambaldi artifact is the key to an apocalyptic event that the agency races to prevent. Also, a monk makes a revelation to Sloane and Dixon tries to deal with his grief over Diane.
Will is suspected of being the second double.
Will is cleared, Syd's mother finally reveals her true motivation, and Syd shoots the evil Francie before waking up two years later to learn that she was thought dead and Vaughn is married.