Steve Zissou (BILL MURRAY) is a famous, 52-year-old oceanographer known for the documentary films made during his crew's various aquatic adventures. During his last one, which resulted in a film not generously received by those who've attended the premiere, Steve's best friend was eaten by what he could only describe as a "jaguar shark."
Wanting revenge, Steve plans on documenting himself and the crew of The Belafonte finding and killing the beast. Among those accompanying him is Eleanor Zissou (ANJELICA HUSTON), his rich wife; German engineer Klaus Daimler (WILLEM DAFOE); physicist and composer Vladimir Wolodarsky (NOAH TAYLOR); safety expert Pelé dos Santos (SEU JORGE); script girl Anne-Marie Sakowitz (ROBYN COHEN); cameraman Vikram Ray (WARIS AHLUWALIA); frogman Bobby Ogata (NIELS KOIZUMI) and sound man Renzo Pietro (PAWEL WDOWCZAK).
Also on board are various outsiders, including bondsman Bill Ubell (BUD CORT), pregnant reporter Jane Winslett-Richardson (CATE BLANCHETT), and the surprise guest, pilot Ned Plimpton (OWEN WILSON) who claims he's Steve's son from a previous, but not serious romantic encounter. To the dismay of Klaus, Steve offers Ned a job on the ship, mainly out of a sense of duty, but also to give him time to figure out if they're really related.
When producer Oseary Drakoulias (MICHAEL GAMBON) can't come up with the funds to finance this expedition and film -- much to Steve's dismay since he's always lived in the shadow of his rich rival and Eleanor's ex-husband, Alistair Hennessey (JEFF GOLDBLUM) -- Ned uses his inheritance to get them on their way. As they head off to find the mysterious shark, Steve must contend with his failing marriage, his and Ned's growing attraction toward Jane, and even a bunch of pilots that intercept their ship.