The series revolves around Juni and Carmen Cortez attending a Spy Academy and leading their own spy team to counter S.W.A.M.P., a new evil counter spy team.
Tropes associated with Spy Kids Mission Critical:
- Card-Carrying Villain: S.W.A.M.P. has "Sinister" right in its name.
- Fun with Acronyms: S.W.A.M.P. stands for Sinister Wrongdoers Against Mankind's Preservation .
- My Brain Is Big: The Leader of S.W.A.M.P. is Golden Brain, and has a bare cranium.
- Spy School: The school that the Protagonists attend.
- Title Drop: The Spy Academy is called Spy Kids Academy.