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THE STORY SO FAR…

Background info on Seasons 1 and 2 of Alias (for those of you who have been asleep for the last 2 years) 
 

Season 1

At the begining of season 1, we meet agent Sydney Bristow, who works for a secret divison of the CIA, called SD6. She is a student at UCLA, and is roommates with her friend Francie Calfo. The also have a journalist friend called Will Tippin. Sydney's boyfriend, Danny Hecht proposes to her, and she reveals to him that she is a spy. He doesn't take this news very well, so they give each other space. He then phones her to tell her he's fine with her being a spy, and SD6 pick up the phone call. When Syd arrives home that evening, she is horrified to find Danny, shot dead in their bath..

Sydney swears to avenge his death, and goes to hound Sloane, the head of SD6. She ends up being pursued by security section, and is resuced by... her father (Jack Bristow), who turns out is also part of SD6, and tells her that they aren't part of the CIA. Syd goes to get something that Sloane wants, to clear her name, and also goes to the real CIA, where she meets her new handler, Michael Vaughn.

Thoughout the season, Sydney goes on various missions for SD6, and the CIA. The main theme throughout the season is the search for 'Rambaldi' artifacts, which are very advanced, and some are also prophecies. 

In the finale, Sydney rescues Will from torture, and goes with Vaughn to destroy 'the circumference'- a rambaldi artifact, which leaves Vaughn apparently dead (drowned) and her captured When she wakes up, she asks her captor some question, but he tells her he isn't 'the man' - the main 'bad guy' in this season, is actually....

Sydney's mom!!! (Laura Bristow, real name Irina Derevko)

Season 2

Season 2 is even better than season 1. It starts where the finale left off- with Sydney just finding out that the man is her mom. Thoughout the season, Sydney discovers more about the truth of her mother, and in a weird twist, Irina Derevko turns herself into the CIA, saying that she wants to cooperate with them. Sydney truly believes her mother is helping the CIA because she's changed (she used to be a KGB agent, which Syd found out in season 1), but Jack (her father) sees right through her charade.

During this season, the CIA bring down the Alliance (the world-wide organisation which SD6 is part of), Sloane disapears, Dixon (Syd's SD6 partner) shots Emily Sloane (Sloane's wife), and Francie is doubled and then murdered and replaced by the double. In the finale, Sydney finds out the truth about the Francie double, who she thought was the real Francie, and they fight, almost to the death. Syd gets knocked unconcious, and wakes up.. in Hong Kong!

She calls the CIA, and they send Vaughn, who has a wedding ring on his finger, and tells her she's been missing for two years, and they all presumed she was dead.....

Season 3

When we rejoin Sydney, she is sitting in front of Vaughn in the safehouse. After asking him some more questions, she says he is a fake and tries to escape, but is shot by a tranq gun by Vaughn.
The next time she wakes up, she is in a hospital, where Weiss fills her in on what is going on. Dixon also comes in to tell her he is the new head of the joint taskforce, and that the main terrorist group at the moment is The Covenant, who may have had a hand in Sydney's disappearence.
 
Sydney rejoins the CIA taskforce and is introduced to the NSC liason- Robert Lynsey (who has put her father in prison for working with her mother). She fakes knowledge of her captors to blackmail Lynsey into releasing her father.
 
Jack tells her he knew she was alive and him and Irina were trying to find her. He shows her a tape of her in her missing time, murdering a russian diplomat.
 
Syd then reunites with Vaughn, who has come back to the CIA after being a French teacher and also meets his wife Lauren Reed, who is the new NSC liason.
 
Sydney and Vaughn go on many missions together, and bump into some old enemies along the way, including Sark (who has escaped from CIA custody) and Allison Doren, who Sydney thought was dead.
 
At the same time, Jack and Sydney are still trying to piece together what happened to her in the past two years while keeping the fact that she murdered the russian diplomat from the NSC (namely, Lauren).
 
As the season progresses, we discover what Syd has been up to in the last two years, and who Lauren is really working for...
 
...watch Season 3 to find out.

Disclaimer:
The TV show Alias is owned by Touchstone television and ABC. A.P.O. is a fan site and is in no way affiliated with ABC or Alias.