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Renowned oceanographer Steve Zissou has sworn vengeance upon the rare shark that devoured a member of his crew. In addition to his regular team, he is joined on his boat by Ned, a man who believes Zissou to be his father, and Jane, a journalist pregnant by a married man. They travel the sea, all too often running into pirates and, perhaps more traumatically, various figures from Zissou's past, including his estranged wife, Eleanor.