Isabella sends a letter to Phineas stating her true feelings about him and Isabella and the Fireside Girls must retrieve the letter before Phineas reads it.
A capsule falls from the sky into Phineas and Ferb's backyard. Doofenshmirtz gets kidnapped by Professor Mystery who is Peter the Panda's real nemesis.
After the defeat of evil Doofenshmirtz, there is a new threat in the 2nd Dimension. Phineas, Ferb, Candace, and her resistance fighters must team up to defeat this new foe.