High above the waters of Sydney Harbour, Nigel, Sprit, Tiller, and Jib, a squadron of storytelling pelicans, introduce us to Marlin and his kid Nemo, two clownfish who live in the Great Barrier Reef ("One Dedicated Father").

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Nemo, who was born with one fin smaller than the other - referred to as a "lucky fin" - can hardly wait to begin the first day of school. An overprotective Marlin struggles to let his kid go for the very first time ("Big Blue World"). Professor Ray whisks Nemo and the other Reef Kids to the Drop-Off for their first educational adventure, causing Marlin to panic.

Upon spotting a mysterious boat lurking just beyond the reef, Nemo's classmates sneak 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").

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In his frantic search for Nemo, Marlin swims into Dory, a friendly yet forgetful 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 finding 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. Members of the Tank Gang reassure Nemo, and with Gill's leadership, they hatch a plan to clog the fish tank and escape into the ocean as a team. With the Tank Gang's help, Nemo successfully jams the tank's filter ("We Swim Together").

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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 ("Just Keep Swimming - Part 1").

Luckily, they reunite with the diver's mask, which has the address of where Nemo was taken. In their excitement over the recovered mask, Marlin and Dory unknowingly swim into a dangerous forest of Jellyfish that sting Dory and overwhelm them both ("Just Keep Swimming - Part 2").

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Although their journey took a wrong turn, Marlin and Dory are rescued by a large colony of Sea Turtles who guide them through the fast-moving East Australian Current. CRUSH, a wise and laid-back sea turtle, gives Marlin some advice on mellowing out and learning to trust his kid ("Go With the Flow").

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After a totally tubular ride through the current, news about Marlin and Dory's trek to find Nemo spreads throughout the ocean, reaching the Tank Gang all the way to the Sydney Harbour Aquarium. While Nemo and the Tank Gang have successfully dirtied up the tank for their escape plan, they are still trapped by an immovable grate blocking the tank's intake pipe. Only Nemo is small enough to swim through the grate, 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 harbor is suddenly interrupted when a giant fishing net appears, sweeping Dory up, along with a mass of FISH. 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 fish 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 explore the big blue world ("Finale - Part 2").