After Roger Rabbit, Bowers worked at Cosgrove Hall on the cult favourite television shows Danger Mouse and Duckula before moving to London to work for Steven Spielberg's Amblimation studio. He worked as an animator on An American Tail: Fievel Goes West, before going freelance to work on advertisements and features. Bowers later returned to Amblimation, to work on early story development, and as a supervising animator on Balto.
After Chicken Run, Bowers moved between Los Angeles and Bristol, working on several DreamWorks and Aardman projects, including the hit 3D animated comedy Shark Tale and the Oscar winning film from Wallace and Gromit, The Curse of the Were-Rabbit, before directing Aardman's first CGI feature, Flushed Away, with Sam Fell.