Gregorio and Ingrid Cortez are rival spies who fall in love. They retire and have two children, 12-year-old Carmen and 9-year-old Juni. They work for the Organization of Super Spies (OSS) doing desk work. The children have no idea of their parents' previous career. Gregorio and Ingrid are called back into the field when agents go missing. The children are left in the care of their uncle Felix. Gregorio suspects that children's television host Fegan Floop has kidnapped the agents and mutated them into his "Fooglies," creatures on his show.
The OSS now has a full child spy section, of which 13-year-old Carmen Cortez and 10-year-old Juni Cortez have become agents. Even though they were the first of the new Spy Kids Division, they are not considered the top spy kids, and soon they face particularly difficult competition from Gary and Gerti Giggles, the children of double-dealing agent Donnagon Giggles, whom Carmen and Juni helped to rescue in the previous film. It is shown that Carmen defends Gary, and has a crush on him, which strains her relationship with Juni.
Juni Cortez, after Spy Kids 2: The Island of Lost Dreams, has retired from the OSS. He now lives a quiet life and works as a private detective, although his salary is very little. One day, he is contacted by President Devlin, former head of OSS, who informs him that his sister, Carmen Cortez, is missing after a mission gone wrong.
OSS agent Marissa Wilson (Jessica Alba) is attempting to capture a criminal named Tick Tock (Jeremy Piven), who purchases a mini-disk stolen from OSS. Despite being nine months pregnant, she continues her pursuit against the admonitions of her boss Danger D'Amo (also played by Piven). Tick Tock is captured and the mini-disk, which contains information on a weapon of mass destruction called Project: Armageddon, is retrieved.
The series centers around brother and sister team Juni and Carmen Cortez as they attend Spy Kids Academy, a top secret spy school for kid agents. When a new counter-spy agency threatens the safety of the world, it will be up to junior spies Juni and Carmen to train and lead a team of fellow Spy Kids cadets against the forces of S.W.A.M.P. (Sinister Wrongdoers Against Mankind's Preservation) and their diabolical leader, Golden Brain. The Mission Critical team may not be ready, but they are the only ones to call when grown-up spies can't do the job.
The children of the world's greatest secret agents unwittingly help a powerful game developer unleash a computer virus that gives him control of all technology, leading them to become spies themselves to save their parents and the world.