In the second season, plotting against rogue agency SD-6 keeps superspy Sydney Bristow almost as busy as negotiating a relationship with her long-lost mother and dealing with her growing feelings for CIA handler Vaughn. What Syd doesn't know is that there are lots more changes (costume and otherwise) ahead of her... it's going to be a long year!
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 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.
Sydney must outwit Sark in order to find a crucial piece of intel. Meanwhile, Jack faces Sydney's mother for the first time in almost 20 years. Will finally meets Vaughn and Sloane is haunted by his wife's death.
Sydney's dealings with her mother lead Jack to take drastic measures to ensure his daughter's safety. Meanwhile Will is confronted by a mysterious woman about resurrecting his story on SD-6.
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's trust in her father begins to fade. Meanwhile, Sydney and Vaughn may have been exposed to a deadly virus while in Taipei; Sloane haunted by Emily's death begins to unravel. Vaughn enlists Will to help research a case.
Sydney races to find a cure for Vaughn, but in order to find the antidote, Sydney must make a deal with Sark that could endanger Sloane's life. Meanwhile, Will continues his research for Vaughn and discovers some disturbing inconsistencies involving 20-year-old standardized IQ tests.
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.
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.
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.
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 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, Vaughn and Jack must determine whether CIA agent Lennox is who he says he is after his deep cover mission is compromised.
Sydney must make a life-defining decision regarding her future with the agency, while Sloane re-emerges and continues his obsessive quest to piece together the mysterious Rambaldi artifacts - with the reluctant aid of a kidnapped scientist. Meanwhile, Dixon's marriage is put to the test after he tells his wife the truth about his occupation.
A mysterious Rambaldi device's powers are finally revealed and Sloane has its secrets. Meanwhile, Vaughn begs Dixon to aid the CIA in rescuing Sydney, Will is called upon to participate in a crucial CIA briefing session, and Sydney senses that Francie is keeping secrets.
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.
A Rambaldi artifact prophesizes that an apocalyptic event will soon take place, and Dixon's grief leads Vaughn and agency psychologist Dr. Barnett to question his intentions, as his thirst for revenge on Sloane intensifies. Meanwhile Sloane receives a life-changing revelation from a mysterious monk in Nepal, Sydney and Dixon hunt for the killer who stole the heart from his victim.
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.