Nemo is a young clownfish who lives with his father Marlin in the Great Barrier Reef. Nemo, despite being hampered by a lame fin, is eager to explore life around the ocean. Marlin, however, is overprotective of him, having lost his wife Coral and all their other eggs in a barracuda attack, leaving Nemo as his only child. On Nemo’s first day of school, Marlin unintentionally embarrasses him, and while Marlin is distracted with the teacher, Mr. Ray, Nemo defiantly sneaks away from the reef toward a speedboat, where he is captured by a pair of scuba divers. Marlin tries to chase the boat and meets Dory, a blue tang who suffers from acute short term memory loss, who accompanies him. During an encounter with three sharks who have sworn to abstain from eating other fish, Marlin notices a diver’s mask that fell from the boat that took Nemo. Marlin and Dory fight over the mask, giving Dory a nose bleed, which sends one of the sharks into a feeding frenzy, and Marlin and Dory narrowly escape, but are knocked unconscious when the sharks accidentally set off an old mine.
Meanwhile, Nemo is placed in an aquarium in a dentist’s office in Sydney, Australia, where he meets the Tank Gang, including yellow tang Bubbles, sea star Peach, cleaner shrimp Jacques, blowfish Bloat, royal gramma Gurgle, and damselfish Deb, led by Gill, a Moorish idol. That night, Nemo learns he is to be given to the dentist’s young niece, Darla, whose rough treatment has killed most of her previous fish. Gill devises a risky escape plan: Nemo, who can fit inside the aquarium’s filter tube, will jam the filter with a pebble, forcing the dentist to put the fish into plastic bags while the tank is cleaned, giving them the opportunity to roll out the window and into the harbour. Nemo attempts the maneuver, but fails and is almost killed, leaving Gill guilt-ridden.
Marlin and Dory wake up unharmed, but the mask falls into a deep sea trench. Swimming after it, Marlin is chased by an anglerfish, while Dory reads the address and recites it repeatedly to commit it to memory. Dory and Marlin receive directions from a school of moonfish, but Marlin disregards their instructions to take what he believes is a safer route, leading them into a forest of jellyfish where they end up unconscious from all the jellyfish stings. Marlin and Dory wake up to find themselves on the East Australian Current with a group of friendly sea turtles including Crush and his son Squirt. Marlin tells them about his quest, impressing them, and news spreads across the ocean, all the way to the dentist’s office, where a pelican named Nigel tells the Tank Gang. Inspired by his father’s bravery, Nemo makes another attempt to jam the filter, and succeeds, and soon the aquarium’s contents are covered in green algae.
Marlin and Dory exit the East Australian Current and are engulfed by a blue whale. Dory communicates with the whale, who carries them to Sydney Harbour and expels them through his blowhole. There, they meet Nigel, who help the pair escape from a group of seagulls and takes them to the dentist’s office. Meanwhile, the dentist has installed a new high-tech filter, the AquaScum 2003, foiling the Tank Gang’s escape. Darla arrives, and the dentist prepares to give Nemo to her. Nemo plays dead to save himself as Nigel causes a disturbance, terrifying Darla and throwing the office into chaos. After the dentist throws Nigel out, Gill helps Nemo escape through a drain that leads to the ocean.
Thinking that Nemo is dead, Marlin abandons Dory and begins his journey home. Marlin’s departure causes Dory to lose her memory. She meets Nemo as he reaches the ocean, but does not remember him. However, Dory’s memory returns when she reads the word “Sydney” on a drainpipe. She reunites Nemo with Marlin, but is caught by a fishing boat with a school of grouper. Nemo enters the net and orders the fish to swim down in order to break the boat’s net so they can escape. After returning home to the reef, Marlin and Dory watch Mr. Ray take Nemo and his friends on a field trip. At the dentist’s, the Aquascum 2003 has broken, and the gang, having been put in bag, roll out of the window and into the sea. Still stuck in bags, they ponder what happens next.