In the year since Spy Kids 2, Juni is now working as a private detective who gets very little profit. One day he gets a call from the OSS who say that his sister Carmen has gone missing. He comes to the OSS and gets reunited with Donnagon Giggles and his wife Francesca, who explain that Carmen was captured by the Toymaker, an evil villain who was trapped in Cyberspace by the OSS years ago but used the time to create "Game Over", a virtual reality video game which he plans to use to escape by trapping the players in level 5 which is unwinnable. Juni agrees to venture inside the game to save Carmen and shut the game down.