When former SD-6 agent, McKenas Cole takes over SD-6, Sydney and Jack must work together to save their co-workers and Sloane. Meanwhile, Will begins to fear his decision of looking into SD-6.
Grad student Sydney Bristow discovers that her unique after-school job as an agent for SD-6, a top-secret division of the CIA, holds some deadly secrets that threaten the security of the free world.
Recruited freshman year, the shy Sydney jumped at the chance to add some excitement to her life. Little did she know how great she'd be at espionage. Today Sydney is no longer shy or alone. Boyfriend Danny has just proposed and her best friend Francie couldn't be happier. Her friend Will, however, has to feign happiness, keeping his unrequited love for her to himself.
Sydney's SD-6 partner, Dixon, a devoted family man, warns her not to reveal her secret to Danny, and Sydney knows that SD-6 leader Sloane would not tolerate a breach of security. Even Marshall, SD-6's highly inventive but socially lacking weapons and gadget maker knows that divulging their identities is strictly verboten.
After Sydney tells Danny, he's murdered and her life is spun sideways. She finds that her estranged father, Jack, is also SD-6 and that the group is not part of the CIA, but actually an enemy of the United States. Sydney seeks the aid of the real CIA and is put under the command of operations officer Vaughn, who enlists her as a double agent. Her mission is to complete her cases at SD-6 while reporting her findings back to the CIA. But when Sydney finds out that her father is also affiliated with the CIA, she begins to question where his true allegiances really lie.