"The Avengers" helmer had joined the project in March last year and was supposed to write, direct, and produce the Batgirl film.
However, the 53-year-old director has announced his decision to leave the project citing story issues as the reason.
"Batgirl is such an exciting project, and Warners/DC such collaborative and supportive partners, that it took me months to realise I really didn't have a story, Whedon said in a statement obtained by The Hollywood Reporter.
Whedon also thanked DC president Geoff Johns and Warners Picture Group president Toby Emmerich, saying "I'm grateful to Geoff and Toby and everyone who was so welcoming when I arrived, and so understanding when I uh, is there a sexier word for 'failed'?"
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