|"Johnny, wait!" – Susan
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|"Johnny X: A New Beginning"|
|Season 3, Episode 13a|
|United States Airdate:||March 1, 2008|
"Johnny Dukey Doo"
"Johnny X: The Final Ending"
Johnny X: A New Beginning is the first part of 39th episode and the 77th episode over all.
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. The story is continued in "Johnny X: The Final Ending".
- 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.