A drama series about a young woman who works as a spy while trying to hide her occupation from her estranged father and her boyfriend. Sydney Bristow, an athletic grad student, has a not-so-typical after-school job -- she's an agent for SD-6, a top-secret division of the CIA.
Sydney and Dixon are sent to Morrocco to investigate a plot to take down the United Commerce organization, leading them to Sao Paulo where Sydney witnesses the organization leader's kidnapping and a explosive device surgically implanted in his chest.
Dixon rescues the Peace leader and removes the device from his chest. Will continues to investigate Danny's death and his source isn't who she appeared to be. Sydney and Dixon are sent to retrieve an inhaler vaccine and she arranges a switch with Vaughn's men. Thinking she disabled the explosives Dixon planted she gets out but he triggers a second set, killing the CIA men.
Sydney's suspicions of her father grow as she suspects he had been repsonsible for the deaths of many CIA agents and her mother 20 years ago. She is sent into an insane asylum to get the location of a grave site by a incarcerated hitman but finds getting out may be impossible as the asylum is run by the K Directorate.
Sydney is suspected of being the mole inside SD-6 and Sloane subjects her toa lie detector test. She tracks down a clock related to the Rambaldi mystery.
Sloane is informed that Sydney is the mole and reluctantly agrees to "solve" the problem. Dixon is seriously wounded on a mission and Sydney may have blown her cover when she calls the CIA to save him. She is later captured by Sloane's men.
Sydney, captured by SD-6 for being their mole gets a reprieve when suspicions are diverted to Russek who is then tortured and killed. It turns out Jack doctored information to save Sydney from meeting the same fate. Jack is sent to Cuba to take out Hassan but offers him a deal on behalf of the CIA. He is captured and as a measure of loyalty is ordered to kill Sydney...
Vaughn suspects that Jack may have been responsible for the deaths of many CIA agents, including Vaugn's father, in an incident years ago and may be a KGB double agent. Jack reveals that it was Sydney's mother who was the double agent and used Jack as a pawn.
A mysterious former agent takes over the SD-6 building in an all-out assault and plans to destroy the building after opening the vault. Sydney and Jack remain the only free agents and must stop the take-over.
Vaughn disobeys order to help Sydney free the captive SD-6 agents and the building during a siege from a rogue former agent.
Sydney and Dixon are sent to Las Vegas to plant a bug on a member of K-Directorate but Sydney must also deal with Francie and Charlie being there at the same time, about to elope despite Sydney's knowledge of his infidelity and in danger of blowing her cover.
Sydney must steal a Rambaldi manuscript from Sloan's personal safe and is invited over for dinner after manipulating his dying wife, Emily for the invitation. The manuscript reveals a blank page 47, that when decoded reveals a prophecy and an image of Sydney.
The Department of Special Research investigates Sydney's connection with the Rambaldi prophecy and take her into custody when they decode enough of the prophecy to indicate she may be a threat to American security.
Sydney is taken into FBI custody and questioned regarding her involvement with the Rambaldi prophecies while Jack and Vaughn work desperately to rescue her and to counter the prophecies before her cover with SD6 is blown.
Sydney's affair with Noah gets complicated when he reveals he has stolen money from SD-6 and want hers to run away with him. Meanwhile, SD-6 plans to follow "Snowman", a hired assasin to lead them to Khasinau. Also, a video reveals Sydney's mother is still alive and that she used Jack to spy on his activities for the KGB. Sydney has a run in with the Snowman and ends up killing him and reveals him to be Noah.
On a CIA mission to get the ampule for decoding Rambaldi text, Sydney barely escapes from a fight with Dixon and he becomes suspicious of her after remebering she used a different code name when she saved his life.
Jack and Sydney race to rescue Will, agreeing to trade the Rambaldi document in Sloan's possession for him. Vaughn figures out what Sydney is up to and agrees to help her destroy a Rambaldi device while Jack does the exchange for Will. Upon destruction the device unleashes a flood that seemingly drowns Vaughn as Sydney is captured. She finds the person in charge hasnt been Khasinau, but rather her mother who finally shows herself.