While oceanographer Steve Zissou is working on his latest documentary at sea, his best friend and chief diver, Esteban du Plantier, is devoured by a 10-meter-long, luminescently spotted creature Zissou describes as a "jaguar shark". For his next project, Zissou is determined to document the shark's destruction.
The crew aboard Zissou's aging research vessel Belafonte includes his estranged wife Eleanor, chief strategist and financial backer; Pelé dos Santos, a safety expert and Brazilian guitarist who sings David Bowie songs in Portuguese; and Klaus Daimler, the German first mate who views Zissou and Esteban as father figures. Minor crew members include Vikram Ray, cameraman; Bobby Ogata, frogman; Vladimir Wolodarsky, physicist and soundtrack composer; Renzo Pietro, sound man; and Anne-Marie Sakowitz, a script girl who is often seen topless. Also included is a recent group of unpaid interns from the University of North Alaska. However, the "Team Zissou" venture has hit a decline; they have not released a successful documentary in nine years.
Ned Plimpton is a longtime Zissou fan whose mother has recently died, who believes that Zissou is his father. After they meet at Zissou's latest premiere, Ned takes annual leave from his job as an airline pilot in Kentucky to join his crew. As Oseary Drakoulias, Zissou's producer, cannot find a financier for their latest documentary, Ned offers his inheritance. Eleanor feels her husband is exploiting Ned and leaves.
A pregnant reporter, Jane Winslett-Richardson, comes to chronicle the voyage. Both Ned and Zissou are attracted to Jane, and a competition develops between them. Klaus becomes jealous of the attention Zissou pays to Ned.
On their mission to find the jaguar shark, the Belafonte steals tracking equipment from a remote station owned by currently more successful oceanographer (also Eleanor's ex-husband and Zissou's nemesis), Alistair Hennessey. They then sail into unprotected waters and are attacked by Filipino pirates, who steal Ned's money and kidnap Bill Ubell, a "bond company stooge" assigned to the project. They are then rescued by Hennessey and towed to Port-au-Patois. Sakowitz, along with all but one of the interns, jumps ship once they reach port.
Zissou persuades Eleanor to rejoin the Belafonte, and then leads the crew on a rescue mission. They track Bill to an abandoned hotel on a remote island, saving him along with Hennessey, whom the pirates have also kidnapped. Ned and Zissou then make one last search for the shark in the ship's helicopter, but the aircraft malfunctions and they crash. Ned dies from his injuries and is buried at sea. Prior to Ned's death, Eleanor revealed to Jane that Zissou is sterile; therefore Ned could not have been his son.
Zissou finally tracks down the shark in a submersible but decides not to kill it, both because of its beauty and not having any more dynamite. At the premiere of the finished documentary (which is dedicated to Ned who is acknowledged as Zissou's son), Zissou receives a standing ovation while waiting outside the theater for the premiere to finish. The crew returns triumphantly to the ship the next day.
Bill Murray as Steve Zissou
Owen Wilson as Edward 'Ned' Plimpton / Kingsley Zissou
Cate Blanchett as Jane Winslett-Richardson
Anjelica Huston as Eleanor Zissou
Willem Dafoe as Klaus Daimler
Jeff Goldblum as Alistair Hennessey
Michael Gambon as Oseary Drakoulias
Bud Cort as Bill Ubell, Bond Company Stooge
Noah Taylor as Vladimir Wolodarsky
Seu Jorge as Pelé dos Santos
Robyn Cohen as Anne-Marie Sakowitz
Waris Ahluwalia as Vikram Ray
Niels Koizumi as Bobby Ogata
Pawel Wdowczak as Renzo Pietro
Matthew Gray Gubler as Niko, Intern (credited as Intern #1)
Antonio Monda as Himself
Isabella Blow as Antonia Cook
Seymour Cassel as Esteban du Plantier