According to The Hollywood Reporter, Time Warner currently holds the broadcast rights for The Clone Wars through this current season only. They have been renewing one-year deals on an annual basis, an approach that has worked for half a decade now.
With Disney now in charge, the Cartoon Network may no longer become the home for the strong performing show that moved to Saturday morning's this season. Disney's CEO Robert Iger mentioned during the investor's call after the sale that Disney has big plans for Star Wars on television including Disney XD, a channel geared toward boys. He did not mention The Clone Wars specifically, but it seems like the perfect match for the channel.
The Clone Wars series has been distributed on Blu-ray and DVD via Warner Home Video. That could also shift to Disney in the near future as the Mouse House closely looks over current Lucasfilm distribution deals that they may want to bring in-house.
A decision regarding where Star Wars The Clone Wars: Season 6 will air its sixth season next fall is expected to come after Season 5 wraps this spring.
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