Season 2 of Alias aired from September 29, 2002 till on May 4, 2003. It featured Sydney's continued work with the CIA, the takedown of SD-6, Sloane's next phase of plans and a deeper delving into the work of Milo Rambaldi.
The second season begins with the introduction of Irina Derevko, Sydney's mother, who soon becomes a vital part of the series. Midway through the second season, the series underwent a "reboot" of sorts with Sydney successfully destroying SD-6 (after gathering valuable intelligence for tactical strikes from an airborne SD-6 server) and becoming a regular agent for the CIA, still in pursuit of former SD-6 leader Arvin Sloane, his associate Julian Sark, and the Rambaldi artifacts. Sydney's friends at SD-6, Marcus Dixon and Marshall Flinkman, are finally made aware of her dual identity and recruited into the CIA. Sydney also begins a romantic relationship with Vaughn, now that their relationship will not endanger them.
In the second half of the season, it is revealed that Francie Calfo, Sydney's best friend, was murdered and replaced by Allison Doren, a woman who was transfigured to look exactly like her. Allison was then in a position to spy on Sydney and Will. The end of the season saw Will critically injured and Sydney killing Allison, then falling unconscious. She awakens two years later in Hong Kong, unable to remember the two years that have passed. She soon learns that her friends and the CIA believed her to be dead, and Vaughn found a new love and is now married.
Season 2 begins at the exact moment that Season 1 left off, therefore in early 2002. Assuming each episode takes place over the course of a week the season ends in late 2002, with a two year jump in the last few moments making it 2004.
This may not be entirely correct because Sydney tells Dixon that she had known the truth about SD-6 for two years. It is possible that the writers forgot about by the time they wrote the "amnesia" plot line.
Similar to Season 1, the majority of the first half of the season sees Sydney undertaking missions with SD-6, only to then plan counter-missions with the real CIA and double-cross the terrorist organization. This is the case up until Phase One, when SD-6 is finally taken down and Sydney begins a regular job at the CIA. Throughout this section she undertakes missions in an effort to stop Arvin Sloane and discovering further mysteries about Milo Rambaldi.
- The introduction of Sydney's mother, Irina Derevko, as a walk-in at the CIA.
- Sydney's continued distaste for Arvin Sloane.
- Francie's confusion over Sydney's lies.
- Will's efforts to deal with the life he has to live after the events of Season 1.
- Vaughn and Sydney's relationship after the destruction of SD-6.
- The death of Francie and her replacement by Allison Doren, unbeknownst to her friends.
- Jennifer Garner as Sydney Bristow (22/22)
- Ron Rifkin as Arvin Sloane (22/22)
- Michael Vartan as Michael Vaughn (22/22)
- Kevin Weisman as Marshall Flinkman (22 episodes)
- Merrin Dungey as Francie Calfo/Allison Doren (21/22) *
- Bradley Cooper as Will Tippin (19/22)
- Carl Lumbly as Marcus Dixon (17/22)
- David Anders as Julian Sark (15/22)
- with Lena Olin as Irina Derevko (18/22)
- and Victor Garber as Jack Bristow (22/22)
- Derric O'Connor as Alexander Khasinau (1/22)
- Greg Gunberg as Eric Weiss (8/22)
- Patricia Wettig as Judy Barnett (4/22)
- Terry O'Quinn as Kendall (16/22)
- Tony Amendola as Tambor Barceló (1/22)
- Wolf Muser as Ramon Veloso (2/22)
- Joseph Ruskin as Alain Christophe (2/22)
- Kevin Sutherland as Agent Blake (7/22)
- Daniel Faraldo as Manolo De Souza (2/22)
- Ira Heiden as Rick McCarthy (7/22)
- James Lesure as Craig Blair (3/22)
- Stephen Markle as Senator Douglas (2/22)
- James Handy as Arthur Devlin (1/22)
- Austin Technor as Dr. Nicholas (2/22)
- Amy Irving as Emily Sloane (3/22)
- Petra Wright as Alice Williams (2/22)
- Michelle Arthur as Abigail (1/22)
- Don Took as Agent Grey (3/22)
- Derek de Lint as Gerard Cuvee (2/22)
- Ric Young as Dr. Zhang Lee (2/22)
- Faye Dunaway as Ariana Kane (3/22)
- Yvonne Farrow as Diane Dixon (3/22)
- Amanda Foreman as Carrie Bowman (2/22)
- Christian Slater as Neil Caplan (2/22)
- Tracy Middendorf as Elsa Caplan (2/22)
- Arthur Young as Aaron Caplan (2/22)
- Jim Hanna as Claus Richter (2/22)
- Jonathan Banks as Frederick Brandon (2/22)
- Angus Scrimm as Calvin McCullough (1/22)
- Ravil Isyanov as Luri Karpachev (1/22)
- David Carradine as Conrad (1/22)
|01||The Enemy Walks In||September 29, 2002|
|Sydney finds herself face-to-face with her mother, whose intentions for her daughter are made chillingly clear. Later, 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.|
|02||Trust Me||October 6, 2002|
|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.|
|03||Cipher||October 13, 2002|
|Sydney must outwit Sark in order to find a crucial piece of intel. Meanwhile, Jack faces Irina for the first time in almost 20 years. Will finally meets Vaughn and Sloane is haunted by his wife's death. Sloane, who drinks only water is seen drinking whiskey in his office.|
|04||Dead Drop||October 20, 2002|
|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.|
|05||The Indicator||November 3, 2002|
|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 Irina to take a fall. Sloane tells Jack the truth about Emily's death.|
|06||Salvation||November 10, 2002|
|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.|
|07||The Counteragent||November 17, 2002|
|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.|
|08||Passage (Part 1)||December 1, 2002|
|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 abandoned facility in Kashmir. Meanwhile, Sloane announces to a suspicious staff that Sark will be working with SD-6.|
|09||Passage (Part 2)||December 8, 2002|
|Sydney and Jack continue on a mission to take control of six nuclear warheads. Irina meets up with Gerard Cuvee and we discover where Irina's loyalties lie. Meanwhile, Sloane informs the Alliance that Emily may still be alive.|
|10||The Abduction||December 15, 2002|
|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.|
|11||A Higher Echelon||January 5, 2003|
|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.|
|12||The Getaway||January 12, 2003|
|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|
|13||Phase One||January 26, 2003|
|Sydney and Jack are confronted by the new director of SD-6, one Geiger, who replaces Sloane, whose whereabouts and intentions are unknown. Sydney and Vaughn lead the team to raid SD-6 and shut down the Alliance.|
|14||Double Agent||February 2, 2003|
|Sydney, Vaughn and Jack must determine whether CIA agent Lennox is who he says he is after his deep cover mission is compromised in Berlin. It is discovered that an agency has built a machine capable of replicating a human being's appearance.|
|15||A Free Agent||February 9, 2003|
|Sydney must make a life-defining decision regarding her future with CIA, while Sloane re-emerges and continues his obsessive quest to piece together the mysterious Rambaldi artifacts -- with the reluctant aid of a kidnapped scientist named Neil Caplan.|
|16||Firebomb||February 23, 2003|
|Vaughn begs Dixon to aid the CIA in rescuing Sydney, Will is called upon to participate in a crucial CIA briefing session, and Sydney notices that something with Francie is not quite right.|
|17||A Dark Turn||March 2, 2003|
|Sydney begins to question where Vaughn's allegiances lie when she learns through CIA Agent Yaeger that he is under investigation. Meanwhile Irina and another crucial Rambaldi manuscript --this one about the secret of eternal life-- are used as bait to try to catch Sloane.|
|18||Truth Takes Time||March 16, 2003|
|Sydney faces off with her mother, while Emily must decide whether to side with her husband or betray him.|
|19||Endgame||March 30, 2003|
|Sydney defies her father in her attempt to rescue kidnapped scientist Neil Caplan, while Sloane, seeking revenge for the assassination of his wife orders that Dixon's wife be taken out.|
|20||Countdown||April 27, 2003|
|A Rambaldi manuscript prophesizes that an apocalyptic event involving a heart will soon take place. An agent is sent after one man in Panama in order to steal his heart. Dixon's grief leads Vaughn and agency psychologist Dr. Barnett to question his intentions.|
|21||Second Double||May 4, 2003|
|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 Di Regno heart, and Sloane makes Jack a business proposal.|
|22||The Telling||May 4, 2003|
|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.|
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