I wouldn't necessarily say it starts in episode 2.5 "Indicator," as Sydney's struggle between wanting to trust her mother and wanting to be a good agent starts the minute Irina wakes into the CIA- but this episode sure does start the dominos a fallin'.
Irina has just given Sydney and Vaughn the location of her organization's operations manual- a hut in the middle of nowhere. Jack is so frustrated by Irina's ability to coax Sydney, that he sets up his wife by rigging the building with explosives. This, of course, threatens her deal with the CIA and Irina is sentenced to death. Meanwhile, Sydney can't believe she fell for her mother's lies and comes running back to daddy. Though Vaughn isn't a huge fan of the woman who killed his father, he still doesn't buy that Irina set them up. Vaughn digs a little deeper and finds that Jack was indeed the one who arranged to have the building wired.
Sydney is then sent on a mission to track down 12 new-generation weapons- which turn out to be 12 children at what looks to be a camp for spies. Sydney recognizes a puzzle at the home of the operation's leader and discovers that she was subjected to invasive tests by Jack in order to protect her from deceit. So, in other words, Jack fought fire with fire- using Irina's deceit as an excuse for his own. Sydney gives Jack what for and writes a letter to save Irina.
Here is Sydney, sitting between her own curiosity about her mother and her duty and loyalty to her country. Her father complicates the situation with his lies and his unstable past with Irina. Jack's bitterness and anger towards Irina only binds Sydney more. I am still trying to figure out how this girl turned out half way normal and with a smile on her face.
We have talked about the Bristow family dynamic numerous times. Jack questions Irina at every turn, Sydney questions herself at every turn- who should she believe? The father she never knew or the mother she never knew? Despite everything, Sydney still does everything in her power to have her father released from prison and her mother's death sentence reversed.
Aside from this game of back and forth- Sydney struggles with her feelings for Vaughn when he becomes sick with the bloody fingernail disease. She watches Vaughn in a vulnerable state, forcing her to recognize her feelings and her relationship with Vaughn. In the end, Sydney risks everything- her position at SD-6 and the life of her enemy, Arvin Sloane to save Vaughn. Does Sydney never get over this in-between? I don't think so. Even in the end, it is implied that Sydney and Vaughn continued to work for the CIA, even after starting a family. This puts Sydney in a position to play back and forth, between spy and parent. Will she morph into the person her father was- using to lies to protect Isabelle and Little Jack? For the hell she gave Jack in the first episodes of the show- it would seem Sydney would be opposed to keeping her children in the dark. However, I think patterns repeat themselves, especially in families and I think after seeing all she has seen, Sydney would be the first to subject her daughter to the same tests in order to protect her.
But alas, we shall never know. Perhaps Isabelle will live a happy normal life- and become an agent on her own.... ha! Right!