The third season of the series was aired on September 28, 2003. This season also had twenty two episodes in it. The third season opens with Sydney trying her level best to find out about the events of the past two years that have taken place in her life. She comes in contact with people who have thought her to be dead. It was later revealed in the series that DNA evidence in a badly burned body confirmed her death to her family and friends. In the first episode of the third season she confronts Vaughan, who, too, had believed her to be dead.

She also comes to know that her father, Jack has been imprisoned and isolated. But as time goes by and as she starts getting a little bit of her memory from her past, the CIA takes her back but accept her on temporary basis. As the season unfolds itself, Sydney comes to know about the truth of the past two years of her life.

It is revealed in the series that Sydney was kidnapped by a terrorist organization called the Covenant, who tried to brainwash her into believing she was an assassin named Julia Thorne. They then forced her to do some most dangerous things as Julia that she would have, otherwise, never done in her life. Now that those things are haunting her she decides to get her memories of the past two years erased. While she is trying to forget some of the deeds she was forced to undertake as Julia and ensures that one of Rambaldi’s most dangerous artifacts would never be found. With a lot happening in her life, she eventually begins to recover and starts working for the CIA. Now that she has started working for the CIA, she comes to know that Arvin Sloane has become a world-renowned humanitarian after being excused from all the charges against him. She also comes to know that Vaughn has married an NSC agent Lauren Reed. It was later revealed in the series that Lauren is also a member of the Covenant and that she shares a romantic relationship with Julian Sark. The NSC plays a role of a government organization that holds enormous unofficial power, with a Guantanamo-like detention facility, that has considerable influence over the CIA, and the organization is determined to get answers for some questionable motives. As the plot moves ahead Sydney learns some astonishing facts about her mother. She discovers that her mother had an affair with Arvin Sloane and the two together had a child also.

Sydney then starts her search for her half sister, Nadia and is ultimately able to rescue her from being killed by the Covenant. As the season comes to an end we see Sydney and Lauren face to face with each other, when Sydney is sent on a mission and there she has to encounter Lauren. They both indulge in a fight and as they fight Lauren in order to make her weak, begin to taunt her by saying that she has information about her past. When Vaughn comes to that place, he comes to know some astonishing facts about his wife. Once Vaughn gets there, Sydney goes to him and gives Lauren a chance to attack on her. Vaughn then shoots Lauren which kills her, but before she dies she gives Sydney the number of a security deposit box where she can find information about her past.

In the last scene of the season we see a shattered Sydney after she has received a shattering revelation that will make her question everything - and everyone - she thought she could trust.

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