The series centers around brother and sister team Juni and Carmen Cortez as they attend Spy Kids Academy, a top secret spy school for kid agents. When a new counter-spy agency threatens the safety of the world, it will be up to junior spies Juni and Carmen to train and lead a team of fellow Spy Kids cadets against the forces of S.W.A.M.P. (Sinister Wrongdoers Against Mankind's Preservation) and their diabolical leader, Golden Brain. The Mission Critical team may not be ready, but they are the only ones to call when grown-up spies can't do the job.

When fourteen-year-old Jarvis Raines gets a chemistry set from his Aunt Marlene for Christmas, he assumes it's just another boring gift. Boy is he wrong! The contents create a chemical reaction that destroys his houseso much for a Merry Christmas! After getting not even an apology from the manufacturer, Knickknack Toys, Jarvis takes them to court, wins, and ends up owning the company!