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.
They are captured by Floop's "Thumb-Thumbs", robots whose arms, legs, and head resemble oversized thumbs, and taken to Floop's castle. Felix is alerted to the parents’ capture, activates the fail-safe, tells the children the truth, and that he is not their uncle but an agent. The house is assaulted by Thumb-Thumbs, and the children escape alone on a submarine set to auto-pilot to a safe house. At the safe house, Carmen unlocks the door using her full name, and the children learn of their parents' past as they decide to rescue them.
Inside of Floop's castle, he introduces his latest creation to Mr. Lisp, small robots in the shape of children. He wishes to replace the world leaders' children with these super-strong robots to control the world. The androids are "dumb", and cannot function outside of their inherent programming. Lisp is furious, demanding usable androids. Floop, along with his second-in-command Minion, interrogates Gregorio and Ingrid about 'The Third Brain'. Ingrid knows nothing of the subject, while Gregorio claims that he destroyed the brain years ago. After Floop leaves, Gregorio reveals to Ingrid that the Third Brain was a secret OSS project he once worked on: an AI brain with all the skills of the entire OSS. The project was scrapped as being too dangerous, but Gregorio couldn't bring himself to destroy the final prototype.
Back at the safe house, the kids are visited by Ms. Gradenko, who claims she works for the OSS and gives Carmen a bracelet as a sign of trust. Gradenko says she wants the Third Brain, but Carmen does not know anything about it. Gradenko orders the house to be dismantled, and Juni sees Thumb-Thumbs outside destroying the submarine. Gradenko's intentions revealed, Juni accidentally exposes the Third Brain, and a chase ensues with Carmen and some henchmen with jetpacks. Carmen eventually gets the brain, and she and Juni escape.
Carmen realizes too late that the bracelet Gradenko gave her was a tracking device, and she and Juni are attacked by their robot counterparts. Though Juni tries to destroy it, he is unable and the androids fly off with the Third Brain. With it, Floop can achieve his goal, but he wishes to continue his children's show. Minion has different plans and takes over, locking Floop into his "virtual room," the chamber where he films his television series. The kids receive reluctant help from Gregorio's estranged brother Isador "Machete" Cortez when they come to his spy shop. When Machete refuses to accompany them, they steal some of his gear and take his spy plane to fly to Floop's castle.
While their children storm the castle, Gregorio reveals to Ingrid that Minion used to work for the OSS but was fired after Gregorio reported him tampering with the Third Brain project. Juni rescues Floop who helps him and Carmen release their parents. Together they trap Minion and, confronting Lisp and Gradenko, the family is beset by all 500 robot children. Isador busts through the window, and joins the family to fight. However, at the last moment, Floop is able to reprogram the robots to change sides. The 500 super-strong robots quickly overpower Lisp and Gradenko.
With advice from Juni, Floop introduces the robot versions of Carmen and Juni on his show. The family's breakfast is interrupted by Devlin, the director of the OSS, who has a mission for Carmen and Juni. Carmen accepts on one condition: that the Cortezes work as a family.
