Ingrid and Gregorio 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. Ingrid and Gregorio are called back into the field when agents go missing. The children are left in the care of Uncle Felix Gumm. Gregorio suspects that a kids’ TV show star Fegan Floop has kidnapped the agents, and mutated them into his “Fooglies,” creatures on his show.
They are captured by Floop’s “Thumb-Thumb” robots whose arms, legs, and head are made of 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. The house is assaulted by Thumb-Thumbs, and the children escape alone on a submarine that’s 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 to sell to his clients. Floop along with his second-in-command Alexander Minion interrogate Gregorio and Ingrid. Floop demands the ‘Third Brain’, but Ingrid has no idea what he’s talking about. Gregorio claims that he destroyed the brain years ago. Thinking the brain must be with the children, Floop sends his minions after them. Gregorio reveals to Ingrid the truth about the Third Brain. It was the codename of a project back when he worked in the science division of OSS. It was to house the skills of all of the world’s best super spies. The project was deemed too dangerous, was scrapped and the materials to be destroyed, but Gregorio couldn’t destroy the brain.
Back at the safe house, the kids are visited by Ms. Gradenko. Gradenko says she works for OSS, and is there to help the children. Gradenko wants the Third Brain, but Carmen does not know anything. 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 jet packs. Carmen eventually gets the brain, and she and Juni escape the Thumbs.