Internationally famous oceanographer Steve Zissou (Bill Murray) and his crew - Team Zissou - set sail on an expedition to hunt down the mysterious, elusive, possibly non-existant Jaguar Shark that killed Zissou's partner during the documentary filming of their last adventure. They are joined on their voyage by a young airline co-pilot who may or may not be Zissou's son (Owen Wilson), a beautiful journalist (Cate Blanchett) assigned to write a profile of Zissou, and Zissou's estranged wife and co-producer, Eleanor (Anjelica Huston).

They face overwhelming complication including pirates, kidnapping and bankruptcy.