The second season of the series began on September 29, 2002. The season had twenty two episodes in it. A number of very important things took place in this season, which was very vital from the point of the view of storyline. The series opens with Sydney getting face to face with her mother, whom she thought to be dead till then. Later, her mother’s intentions become clear to her. Sydney’s mother soon becomes a vital part of the series. Next, in the series we find Sydney looking for Vaughn, as she is not sure about his existence.

Will gets a shock of his life when he learns the truth about SD-6 and Sydney’s life as a double agent. With Sydney still getting crushed between her personal and professional life, there are a number of things she has decide about her mother and her attitude towards her. The next very important thing that takes place in the series is that Sydney is able to fulfill her mission of destroying SD-6. She is able to do so after gathering valuable intelligence for tactical strikes from an airborne SD-6 server. After completing her mission, Sydney starts working as a regular agent for the CIA. When the real identity of SD-6 and Sydney is revealed to all Sydney’s friends at SD-6, even they are recruited into the CIA. Meanwhile, Sydney’s father Jack is not very happy with the fact that Sydney is getting that close to her mother and decides to take some safety measures for her.On the other hand Sydney also starts a romantic relationship with Vaughn, now that she is sure that nothing will affect their relationship and that their relationship will not endanger them.

Through out the series we see Sydney constantly fighting with herself about her father and mother’s true identity. Quite late in the second season she realizes the true intentions of her mother. It is then revealed in the series that Francie Calfo, who was Sydney’s best friend, was murdered and replaced by Allison Doren, a woman who was transfigured to look exactly like her. It was only then that Allison was in a position to spy on Sydney and Will. In the last episode of the series we find Will struggling to find the fact who was behind this whole setup.

In his this effort we see Will possibly losing his life and Sydney is able to take her revenge on Allison by killing her. In the whole fight that takes place between Allison and Sydney, Sydney gets hurt badly and we see her losing unconscious. In the last scene of the episode we find out that two years have already passed and Sydney has lost account of two years of her life. Sydney awakens two years later in Hong Kong, and is unable to remember the two years that have passed. But when she gets back her memory and remembers about her past life, she soon learns that her friends and the CIA believed her to be dead. This is already very hard for her to accept when she finds that her then boyfriend Vaughn has also moved in life and has found a new love for him and that he is now happily married to someone else.

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