Internationally reknown oceanographer Steve Zissou and his crew - Team Zissou - set sail on an expedition to hunt down the mysterious, always elusive, possibly non-existant Jaguar Shark that supposedly killed Zissou's partner during the documentary filming of their latest adventure. On this journey, Steve's crew are joined by a young airline co-pilot, who may or may not be Zissou's son, a beautiful journalist who has been assigned to write a profile of Zissou, and Eleanor, Zissou's estranged wife and co-producer. They face overwhelming complications including pirates, kidnapping, and bankruptcy.