In ancient feudal China, Princess Isabella is part ruler and Master Perry has given up the way of the warrior. After Phineas and Ferb witness Doofus Khan capture the Princess and take her as a prisoner, they track down Master Perry and convince him to teach them his warrior ways so they can rescue Princess Isabella and save China.

After locating and retrieving the Amulet of Juatchdoon, adventuring archeologist duo Ohio (Phineas) Flynn and Rhode Island (Ferb) Fletcher set off to South America to help Damsel in Distress Isabella find the Lost Temple of Juatchadoon and her missing mother. However, Dr. Doofenshmirtz has other plans for the amulet - to awaken the evil corn colossus to give him the power to destroy the world.