|"Johnny, wait!" – Susan
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|"Johnny X: A New Beginning"|
|Season 3, Episode 13|
|United States Airdate:||March 1, 2008|
"Johnny Dukey Doo"
"Johnny's New Baby Sisters"
Johnny X: A New Beginning (JX6) is the 39th episode and the 77th and 78th episode overall. It is an extended episode.
It's time for the Earth Day Carnival, and the Johnny Stopping Evil Force 5 (with Zizrar replacing the Beekeeper) returns and manages to obtain the same mutant powers as Johnny X and Super Dukey. Meanwhile, Dark Vegan returns to conquer Earth.
Dark Vegan returns to destroy the Earth with an upgraded armada. Dark Vegan, with his upgraded armada, is cutting up the Earth's trees and plants (which will remove the oxygen) and sucking up the Earth's water and killing the trees.
- After the events of "Johnny Holiday", it is revealed that The Bee Keeper has resigned from the Johnny Stopping Evil Force 5, with Zizrar taking his place.