CatDog: The Great Parent Mystery (2001 TV Movie)
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(Warning: contains spoilers) In this movie, after being completely stray from their origins and family, CatDog decide to set out to find their long-lost parents. During the trip, they face a few odd ball characters like aliens, a giant lake monster, and a bunch of hillbillies. During their visit with the aliens, the audience is given what seems like a history of where CatDog might have come from. In the mothership of the aliens that CatDog go into (to find their parents), there are a bunch of exotic creatures on the ship that seems to be mixed together with other exotic creatures.
Then at the end, CatDog end up finding their parents and soon discover that their mother is a giant Bigfoot, and their dad, who's voiced by Academy Award nominee Billy Bob Thornton, is small, lowbrow frog.
I'd say this was a good way to end the series. CatDog find their family and the bad guys of the show, the Greaser Dogs, get beaten in end.