In the commentary for the season 2 finale episode "The Telling," they talk about how they filmed a few different reactions for Syd hearing for the first time she's lost 2 years of her life in addition to the love of her life. Screaming, denial and violence were all options, but in the end it was sheer shock registering on her face before the ALIAS credits appeared. IMO it was the best way to handle the scene, considering that's how the fans must have felt. How did you all react the first time you saw this cliffhanger ending?
The entire finale episode is packed full of action, tension and suspense. Will comes so close to figuring out who the second double is, Syd is on the verge of capturing both Sloane and Irena, and Jack is taken hostage and is helpless to stop Sloan from finishing the Rambaldi Device. In a way, the one stable thing throughout the episode is the relationship between Syd and Vaughn as they try to plan a vacation to Santa Barbara. This certainty is torn away when we see Vaughn struggling to tell Syd what's going on at the end and happens to wipe his face with his left hand, revealing a wedding ring.
The beginning of season 3's "The Two" gives the viewer a false sense of relief as Syd beats the crap out of Vaughn thinking he's a double as the real Vaughn would never be married to someone else. Unfortunately Dixon informs her of the truth in the hospital; Vaughn is indeed married, she's been presumed dead for almost two years, Jack is in solitary prison and Will is in witness protection. There are many heart wrenching scenes in this eppy, from Syd's visit with Jack (you probably know this, but I love you), to her confrontation of Vaughn in the hospital (you wanna know how I am?? I am HORRIBLE...ripped apart!) There is a small amount of resolve at the end when Jack is freed and reunited with Syd, only to show her a video of a woman slitting a Russian diplomat's throat who turns out to be her. Can you even imagine seeing yourself do something like that and not remembering??
Overall I think the flow from season 2 to 3 was smooth, though heartbreaking given Syd's new life. The only let down I felt was the build up of the Rambaldi Device in season 2 and finding out all it did was rumble and shake only to write out the word "Peace." Ah well, what did you all think?