Carmen (ALEXA VEGA) and Juni Cortez (DARYL SABARA) are some normal kids who think they have normal, everyday parents. Unbeknownst to them, however, their father, Gregorio (ANTONIO BANDERAS), and mother, Ingrid (CARLA GUGINO), were formerly super spies who once hunted down each other, before falling in love, settling down and starting a family.
Now nine years after they gave up the spook business, they've received news that various OSS agents have been disappearing, with Gregorio suspicious that they've been converted into cartoon like characters on a popular TV kids show hosted by Fegan Floop (ALAN CUMMING). Accordingly, they set out to uncover the truth and so call in "Uncle" Felix (CHEECH MARIN) to watch over the kids.
It's not long after that, however, that Felix receives a distress call and informs the kids of the truth, all while battling some villains and sending the kids off in an escape pod headed for a "safe house." Armed with the message that "the third brain lives," and suddenly thrust into the roles of being their parents' rescuers, Carmen and Juni try to figure out what's going on, and begin piecing together the story when Ms. Gradenko (TERRY HATCHER) shows up with a collection of henchmen, claiming to be an OSS agent and longtime friend of their parents.
They soon realize that Gradenko is a villain who's after the miniaturized brain for Floop and his right-hand man, Minion (TONY SHALHOUB), who need the brain to complete the army of child robots they're building for head villain, Mr. Lisp (ROBERT PATRICK). After a chase and several close calls, the kids learn more information from their estranged Uncle Machete (DANNY TREJO) and then set out to battle the robot kids - two of which are exact copies of them - stop the villains, and rescue their parents.