Renowned oceanographer Steve Zissou is both celebrated and criticized for his eccentric, often reckless deep-sea explorations. After a jaguar shark kills his longtime friend and partner, Steve vows to hunt down and kill the creature. He forms Team Zissou, consisting of his loyal crew and a fresh-faced bond company stooge named Ned Plimpton, who might be Steve's son. Eleanor, Steve's estranged wife, and Klaus, his devoted first mate, also join the mission. As they navigate the treacherous waters on their ship, the Belafonte, the team faces financial troubles, rivalries, and dangerous sea creatures.

The journey is filled with quirky encounters and unexpected challenges, further complicated by Steve's insecurities about aging and his legacy. The crew contends with pirates, mechanical failures, and their own interpersonal dramas. Their quest for revenge pushes them to their limits and forces them to confront their pasts, relationships, and what it truly means to find closure. With the fate of Team Zissou hanging in the balance, Steve must reconcile with his identity as an explorer and a leader.