Carmen (Alexa PenaVega) and Juni Cortez (Daryl Sabara) live with their parents, Ingrid, and Gregorio, who they believe are boring, unaware that their parents are actually semi-retired international spies Grogorio Cortez (Antonio Banderas) & Ingrid Cortez (Carla Gugino), working for an organization called the OSS (Organization of Super Spies). Originally, Ingrid and Gregorio were enemies until they fell in love and got married. They retired to some degree when they had their children. Long ago, at a time of unstable relations between countries, a new breed of soldiers was created: super spies. Using their vast intellects and prowess in the art of stealth, they could stop wars before they even happened. The two protagonists of the story, both of whom were spies, were tasked with eliminating each other, but they ended up becoming infatuated with one another instead and soon fell in love. Despite being from opposing nations, they decided to marry, but this only painted a massive target on their backs for enemy factions that wished to see them dead. They ultimately chose to retire and start a family. They shield their children from their secret spy lives to protect them from inherent danger. The parents are worried about their kids as according to their school principal Carmen's been skipping out on school and Juni's self-proclaimed 'friends' are only in his head. Carmen's main concern in life is with the unwelcome responsibility of babysitting her brother, Juni, and is therefore usually mean to him. However, underneath her abusive exterior, Carmen is hiding secrets of her own: she skips school and has to wear diapers at night due to having problems with bed-wetting. She is desperate to keep both of these problems secret, especially from her brother. Juni lacks self-esteem and is a fan of a children's television show called "Floop's Fooglies." Hosted by Fegan Floop (Alan Cumming) and co-starring the Fooglies-colorful, mutant, gibberish speaking friends of Floop-the show proves to be an irritant to Gregorio, who openly displays his dislike for the program. Gregorio receives information from the OSS that several of their agents have gone missing, notifying Ingrid the following morning. Gregorio and Ingrid are suddenly called back to active field work to find missing agents. Gregorio suspects children's television host Fegan Floop has kidnapped them. Georgio takes notice that one of Floop's side characters, called 'Fooglies,' looks suspiciously like one of the missing OSS agents, Donnagon Giggles (Mike Judge). Gregorio suspects the show is involved in the disappearance of several fellow spies mutating them into his "Fooglies" - creatures on his show, a program that Juni avidly watches. Ingrid and Gregorio decide to investigate and leave their children in the care of "Uncle" Felix Gumm (Cheech Marin), a man not actually their uncle but, rather, a family guardian. Gregorio and Ingrid take a mini-sub and head to Floop's suddenly pick up a transmission from Floop, telling them they have something he desires, and they find themselves being chased by a sub. Gregorio tries to outrun it, but soon he and Ingrid end up getting engulfed by a much larger sub. Ingrid and Gregorio are captured by Floop's men, the ever-idiotic Thumb-Thumbs, robots with thumbs for legs, arms and heads that wear red vests. Carmen and Juni discover the truth about their parents when they find that their parents have been kidnapped. In Floop's island castle, Floop is in a pickle of his own. He is being contracted by a businessman named Lisp (Robert Patrick), the head of a nameless corporation, to build an army for them, and so far, the candidates he's given them (The Fooglies and Thumb-Thumbs, additional characters from the show) have been unsatisfactory to their liking. Floop then presents them with his newest invention, Spy Kids, an army of super-strong robots, using the children of world leaders as a disguise, to conquer the world. The robots were constructed by Floop's servant Alexander Minion (Tony Shalhoub). Since the androids have no artificial intelligence yet, they are unable to function outside their regular programming. An item named the Third Brain is required to power the robots, or at least give them the ability to speak and think. Lisp is furious, demanding usable androids. Lisp chastises Floop for not keeping with their schedule, and demands that he finish his army in two days or everything he's built will be reduced to ashes. Ingrid and Gregorio were brought in, due to Gregorio being one of the scientists who created the Third Brain and hid it, although he refuses to give the hiding place. Ingrid knows nothing of it, while Gregorio claims he had destroyed the brain years ago. After Floop leaves, Gregorio reveals to Ingrid that the Third Brain was a secret OSS project he had worked on: an AI brain with all the skills of the entire OSS. The project was scrapped as being too dangerous and many scientists demolished the brains that they were working on, but Gregorio refused to destroy the final prototype. Floop's minions invade the Cortez home, although Carmen and Juni escape whilst Felix is captured, but not before he tells the children the truth about their parents. The children escape alone via a miniature submarine set to autopilot to a safe house. At the safe house, the children accept that their parents were spies and decide to rescue them. The children flee to a safe house where they decide to become spies, until Ms. Gradenko (Teri Hatcher), a fellow spy, arrives to help them. Giving Carmen a bracelet as a sign of trust, she asks about the Third Brain, but Carmen is confused. Gradenko orders the house to be dismantled and the siblings realize Gradenko is a traitor when they see ninja Thumb-Thumbs destroying the escape submarine. It is revealed that Third Brain is hidden in the house. Juni accidentally exposes the Third Brain, and a chase ensues. Carmen gets the brain, and she and Juni escape. She realizes too late the bracelet from Gradenko has a tracking device. The children escape but soon encounter robotic clones of themselves who steal the Third Brain and deliver it to Minion, who takes command of the robots and imprisons Floop. Meanwhile, back at the castle, Gregorio tells Ingrid that Minion used to work for the OSS, but was fired after he reported him tampering with the Third Brain project. With it, Floop can achieve his goal, but he wishes to continue his children's show. Carmen and Juni locate Gregorio's estranged older brother and inventor, Isador "Machete" Cortez (Danny Trejo), who harbors bitter feelings against his younger brother, similar to the feelings Carmen harbored toward Juni. Machete was apparently forced to watch over Gregorio and left him because of this. He refuses to help the children because of this. With no support from their uncle, the children sneak away to rescue their parents on their own, stealing a map of Floop's castle and a spy plane to get them there. Their sibling rivalry comes to a head, however, when Carmen's continuing criticisms and name-calling pushes Juni to retaliate by calling her "diaper lady," starting a quarrel that almost crashes the plane. As they work together to safely land the craft, Juni reveals that he had always been aware of Carmen's nighttime bed-wetting but kept that knowledge to himself at their mother's insistence. Having come to an understanding of each other as brother and sister, their relationship begins to improve from this point on. The two make it to the castle and search for their parents. Juni finds Floop and frees him, convincing him to help them and explaining what was missing from his TV show- children. Carmen, Juni and Floop free Ingrid and Gregorio and then confront Minion, trapping him in a machine that creates the Fooglies on the children's show (who are actually the missing agents). Minion deliberately starts the machine but escapes before he becomes a Fooglie, altering his appearance with three extra heads and combined hands with multiple fingers. The spies confront Gradenko, Minion and Lisp and are attacked by their 500-man army of child robots. Machete arrives to help, later on claiming he came back for the same reason he left, meaning that he was told to watch over his brother. Floop rewrites the children's minds to make them act like children (as Minion says to Lisp, "They have minds of their own now, sir; anything we tell them to do goes in one ear and out the other!"), saving the Cortez family and causing the children to play with Gradenko, Minion and Lisp, tossing them around in the air. Gregorio and Machete reform their brotherly relationship, with both of them claiming neither of them even remembering why Machete left, and Floop redesigns his show with Minion and the robotic Carmen and Juni as his new characters. The leader of the OSS, Devlin, offers the Cortez children jobs as spies, to which Carmen responds that the spy-work is easy, whilst keeping their Cortez family together is the hardest mission of all. Having adopted a stronger value of family unity, she demands that they be allowed to work together as a family.
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