
Season 3 - Summary
Sydney returns home, still reeling from the knowledge that she's been missing, thought dead, for two years, and that Vaughn has married someone else. Francie is dead; Will is in Witness Protection, her father is in prison and her mother is still at large. Dixon has taken over as Director of the Joint Task Force, and the NSA has exerted a rather strong presence into their operations. To top it off, Sloane has been pardoned and is now heading up a worldwide relief organization and assisting the CIA as needed. In other words, her entire world has been turned upside down, and she has no memories of the last two years.
Needing her father to help her make sense of her missing years, she immediately manipulates the NSA director, Robert Lindsay, into granting his release after being held in solitary for a year. Together, they resume Jack's previous investigation into her disappearance, while Sydney struggles to adjust to her surroundings... being re-partnered with Vaughn and having to work with his wife, NSA agent, Lauren Reed, not to mention seeking help from her arch-enemy, Arvin Sloane.
The further they dig, the more puzzling their questions become, and Jack struggles to protect her from life-threatening procedures that the NSA wants to employ in order to recover her memories, believing that she is the key to something that they need. Finally, they take her into custody, and it's up to Jack and Vaughn, along with the help of Sloane to rescue her.
Eventually, the pieces of the puzzle begin to take shape, although many questions are left unanswered. Sydney gets a surprise visit from Kendall, who reveals he that he is actually the Director of Special Research, not FBI, as they'd always been led to believe. He helps Sydney fill in the blanks regarding her missing time, and she learns that she is in fact responsible for her memory loss.
The roller coaster ride continues as it is revealed that Lauren is actually a double agent whose true allegiance is to the Covenant, the Rambaldi-obsessed organization responsible for Sydney's disappearance. Having grown ever closer since her return, Vaughn and Sydney struggle to find their way back to one another in the midst of all the betrayal and deceit surrounding them. In another shocking revelation, Sloane reveals that he and Irina had had a brief affair before her extraction, and that their union produced a child... the "Passenger" as identified by Rambaldi's prophecy. He implores Jack and Sydney's help in locating and recovering her, which they do.
As the season winds down, Sydney and Lauren battle to the death, with Vaughn arriving to deliver the final blow. However, before her death, Lauren reveals to Sydney the location of an important piece of information that she claims holds the key to Irina's whereabouts, and ultimately the identity of the person she claims is controlling the strings of Sydney's life. Sydney goes there and discovers a secret so shocking that once again, the very foundation of her life is shaken to its core.