In the warm, tropical waters of the Great Barrier Reef, members of the Sea Chorus relish in the beauty of their underwater paradise, including two clownfish and soon-to-be-parents, Marlin and Coral ("Prologue"). Tragically, a vicious Barracuda attacks, leaving Marlin alone with all but one of their eggs, a child he names Nemo.

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Time passes, and Nemo excitedly arrives at the schoolyard for the first day of school, where it is revealed that Nemo was born with one fin that is smaller than the other, referred to as a "lucky fin." An overprotective Marlin struggles to let his kid go for the very first time ("Big Blue World - Parts 1 and 2"). Professor Ray whisks Nemo and the other students off to the edge of the coral reef, causing Marlin to panic ("The Drop-Off"). Upon spotting a mysterious boat lurking just beyond the reef, Nemo's classmates swim towards it, daring each other to go further into the deep water. When a terrified Marlin arrives and scolds the children, Nemo defiantly charges further out and is captured by a diver's net ("Abduction / Big Blue World - Reprise").

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In his frantic search for Nemo, Marlin swims into Dory, a friendly yet forgetful blue fish who offers to help ("Dory's Ditty"). Unknowingly, Marlin and Dory float into shark territory, where they meet Bruce, a great white shark, and a whole frenzy of sharks trying to adopt fish-free diets ("Fish Are Friends Not Food"). Amidst the sharks' gathering, Marlin spots a diver's mask lying on the ocean floor, and Dory turns to the sharks for help reading the inscription, hoping it will offer a clue to find Nemo. Doubting her judgment, Marlin struggles with Dory over the mask, accidentally causing her nose to bleed. The scent of blood ignites Bruce's insatiable appetite for fish, and while Marlin and Dory escape, they lose the diver's mask in the process.

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Meanwhile, in a tank at the Sydney Harbour Aquarium, a scared Nemo longs for home ("Where's My Dad?"). Members of the Tank Gang reassure Nemo, hatching a plan to clog the fish tank and escape into the ocean as a team ("We Swim Together"). Nigel, a fish-friendly pelican, promises to keep an eye out for Nemo's dad in the sea.

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Back in the ocean, Dory tries to cheer Marlin up as the search for Nemo continues, but Marlin is frustrated by her quirky antics. Luckily, they reunite with the diver's mask, which has the address of where Nemo was taken. Though Marlin would prefer to go on alone, the two head off towards Sydney with the generous assistance of a school of Moonfish ("Just Keep Swimming - Part 1"). After an argument over which direction to travel, Marlin's choice wins, leading the duo into a dangerous swarm of Jellyfish that sting Dory and overwhelm them both ("Just Keep Swimming - Part 2").

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Back at the aquarium, Nemo and the Tank Gang have successfully dirtied up the tank for their escape plan but find they are still trapped by an immovable grate blocking the tank's intake pipe. GILL, who like Nemo has one different fin, promises they can hatch a new plan. Nemo fears an escape is hopeless, doubting that Marlin is even out there searching ("Not My Dad").

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Back in the ocean, a large colony of Sea Turtles rescues Dory and Marlin from the jellyfish and guides them through the fast-moving East Australian Current. Crush, a wise sea turtle, gives Marlin some advice on mellowing out and learning to trust his kid ("Go With the Flow"). After a totally tubular ride through the current, word spreads throughout the ocean about Dory and Marlin's trek to find Nemo ("One Dedicated Father").

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Nigel flies to the tank to deliver the exciting news that Marlin has reached Sydney Harbour, and Nemo beams with pride ("That's My Dad"), but the appearance of an aquarium net threatens to stop Nemo from escaping. Determined to get Nemo back out to sea, the Tank Gang works together to break free of the net and coaches Nemo to swim through the grate and up the intake pipe ("We Swim Together - Reprise"). They know that they'll join Nemo out in the ocean someday.

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In the ocean, Marlin worries that all hope is lost when, suddenly, Nemo flies out of the tank pipe! Their happy reunion in the harbour is suddenly interrupted when a giant fishing net appears, sweeping Dory up, along with a school of Moonfish. Having learned from the Tank Gang how to free them, Nemo swims into the fray and instructs the captured fish to swim down together, guiding Dory and the Moonfish to freedom ("Just Keep Swimming Together"). With admiration for each other's bravery, Marlin and Nemo make their way home with their new friend Dory ("Finale - Part 1").

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With faith in Nemo to take on all the adventures that await in the ocean, Marlin and Dory send Nemo off to school to go explore the big blue world ("Finale - Part 2").