 While making a documentary, the famous oceanographer Steve Zissou (Bill Murray) loses his dear friend, eaten by a jaguar shark. He raises funds for an expedition in his ship Belafonte to hunt the shark and make a new film. The journalist Jane Winslett-Richardson (Cate Blanchett) and a pilot that claims to be his unknown son, Ned Plimpton (Owen Wilson), join his crew in their journey, planned by his wife Eleanor Zissou (Anjelica Huston). While making the movie, they are attacked by pirates and left without any money to finish their work.