It's up to Timmy to save the universe from the Darkness, a large black hole that could destroy the universe by sucking out all the light and magic in it. Jorgen then sends all the fairies to Earth in order to hide. Timmy then sees some anchient cave drawings that claim that he is the "Chosen" sent to defeat the Darkness by finding three powerful magic wands with the help of Cosmo, Wanda, and Poof, but the Darkness then sends his minions, the Eliminators, to hunt Timmy down throughout the universe to destroy him before he could find those wands.

Timmy learns he merely slowed down The Darkness and now he must seek a second wand to defeat this evil force. Timmy is forced to make amends with his enemies in order to fight for the betterment of mankind.

Confident and secure, Timmy feels great after defeating The Darkness as his world turns into a paradise for him; however, he soon discovers that it is all an illusion and that he didn't win, but is now living inside The Darkness. Now his family, his friends, and even his enemies on the outside must rescue him and help him find the third and final wand in order to defeat The Darkness once and for all.