Plot

Marlin (Albert Brooks) and Coral, a clown-fish couple, live happily in an anemone in the Great Barrier Reef. They are about to become parents, waiting for their many eggs to hatch. Excited to be first-time parents, they discuss names, Coral expressing her fondness for "Nemo." Suddenly, a barracuda approaches the anemone. Ignoring Marlin's order to hide, Coral rushes to protect her eggs as the barracuda knocks Marlin unconscious. Upon awakening, Marlin discovers that Coral (Elizabeth Perkins), and most of their eggs are killed in the barracuda attack. Only one damaged egg with a scratch on its right side remains, and Marlin names his child Nemo (Alexander Gould), a name Coral liked, and vows to keep him safe.

Years later, Marlin is overprotective of Nemo. Nemo grows up with a tiny right fin. Marlin helps him prepare for the day, showing to be overprotective and doubtful of Nemo's ability to take care of himself. On Nemo's first day of school, Mr. Ray (Bob Peterson), the local teacher, takes the children on a field trip. When Marlin learns that they are going to the drop off, he swims after them in a panic. Upon arrival Nemo follows three of his peers (Jordan Ranft, Erica Beck, and Erik Per Sullivan), bored with Mr. Ray's lesson, to the very edge of the reef where they see a boat anchored in the distance. They dare each other to swim out into open water to touch the boat. Marlin arrives and yells at Nemo for endangering himself.

While Marlin is talking to Nemo's teacher, Nemo defiantly approaches a nearby speedboat, where he is captured by a pair of scuba divers. Marlin is prevented from swimming out after his son by another diver who takes a picture, disorienting him. The diver places Nemo in a cooler full of water and accidentally drops his mask into the water. Marlin pursues the boat in vain and meets Dory (Ellen DeGeneres), a blue tang, who offers her help. She claims to have seen the boat and leads a thankful Marlin in the direction it went but, as they swim along, she becomes lax and even tries to evade Marlin when she notices him behind her. When she confronts him, he questions her and she apologizes, telling Marlin she has short-term memory loss.

The two encounter three sharks Bruce (Barry Humphries) a vegetarian great white shark, who fights his instinctive wills to eat innocent fish, Anchor (Eric Bana) a hammerhead shark and Chum (Bruce Spence) a Mako shark who've sworn to abstain from eating fish. Despite Marlin's objections, escorts them to his lair in a sunken submarine surrounded by live sea mines.

The two are fairly terrified by the sharks until Marlin spots the diver's mask stuck on a shard of metal. Dory picks up the mask to see if the sharks can read but Marlin tries to take it back, engaging in a tug-of-war before the mask snaps into Dory's face, causing a nosebleed. The scent sends one of the sharks into a feeding frenzy, but they flee after accidentally setting off a ring of old naval mines, which knock Marlin and Dory unconscious.

Meanwhile, Nemo is placed in an aquarium in a dentist's (Bill Hunter) office in Sydney, Australia. He meets the "Tank Gang", including yellow tang Bubbles (Stephen Root), starfish Peach (Allison Janney), the French-accented Pacific cleaner shrimp Jacques (Joe Ranft), blow-fish Bloat (Brad Garrett), royal Gramma Gurgle (Austin Pendleton), and damsel-fish Deb (Vicki Lewis) a black-tailed humbug who believes her reflection to be her twin sister Flo, led by Gill (Willem Dafoe), a Moorish idol. A pelican named Nigel (Geoffrey Rush) perches himself on the window near the tank and greets Nemo after briefly discussing dental procedures with the other fish.

Nemo learns he is to be given to the dentist's niece, Darla (LuLu Ebeling), who has killed her previous fish. Afraid and wanting to go home, Nemo backs away and gets stuck in the suction tube of the filter. The other fish go to help him but Gill, a wise Moorish idol with large scars on his right side, tells Nemo that he must escape himself, giving Nemo instructions and encouragement. Nemo manages to free himself and Peach relates his strength to his ocean origins, like Gill.

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 he cleans the tank, giving them the opportunity to roll out the window and into the harbor. Though the other fish are skeptical, Gill asserts that Nemo is small enough to fit into the filter and make it back through the tubing. Nemo agrees to do it.

Gill tosses him a pebble and gives instructions as Nemo wedges the fan, stopping the flow of water. However, as he is moving through the pipe back into the tank, the pebble unhinges and the fan turns on again, sucking Nemo backwards. The other fish hurry and send Nemo a toy kelp strand to grab onto and pull him out. This incident causes Gill to feel deeply regretful.

Marlin and Dory awake in the aftermath of the explosions to find the submarine hanging precariously over the edge of a deep ravine. Their movements cause the submarine to suddenly tip forward and collide with the rock wall of the far side. During the chaos and blinded temporarily by the dust, Dory accidentally drops the mask into the darkness below.

They descend after it and encounter an angler-fish which chases them. Dory memorizes the address written on the goggles, and they escape. Dory recites the address 'P. Sherman 42 Wallaby Way, Sydney' and is ecstatic to find that she can remember it.

Dory and Marlin receive directions from a school of moon-fish (John Ratzenberger), but Marlin disregards them to take what he believes is a safer route. They stumble into a forest of jellyfish. Finding that the tops don't sting, Marlin and Dory bounce on them as they race out of the school. Marlin makes it out first and, when Dory doesn't appear, goes back in to retrieve her. He finds her unconscious and scarred from the stinging and struggles to carry her out as he is repeatedly stung. He makes it but, stung and exhausted, blacks out as a large shadow descends on him.

They awaken in the East Australian Current with a group of sea turtles including Crush (Andrew Stanton) and his son, Squirt (Nicholas Bird). While playing with the other sea turtles, Squirt is accidentally propelled outside the current. Marlin is panicky at first however Crush convinces him that Squirt can handle himself. Squirt is able to swim his way back into the current & gleefully joins his father. Marlin sees that even the youngest among the turtles can learn to survive in the ocean. Marlin tells them about his quest. His story is not ignored; it's passed on from turtle to fish to dolphin to bird and onward. The story travels across the ocean to Sydney where a pelican, Nigel hears it and tells the Tank Gang. When Nigel suggests that Nemo's father took on three sharks and a school of jellyfish, Nemo is newly impressed with his father. Invigorated, Nemo takes it upon himself to try the filter attempt again and, this time, succeeds.

Marlin and Dory exit the East Australian Current. They are instructed to continue through a large purplish plume of plankton to Sydney. However, they soon become lost, and Dory resolves to ask a distant fish for directions. Though Marlin is afraid at first, he decides to trust Dory and she calls out to the distant figure. When she sees its a Minke whale, she starts speaking 'whale', asking for help. Marlin grows frustrated with her again just as a whale approaches from behind and pulls them into its mouth.

In the whale's mouth, Marlin and Dory remain safe with enough water to swim in. Marlin yells at Dory for claiming to have spoken whale, calling her insane and lamenting over the fact that he'll never see his son again. Dory tries communicating with the whale, which expels them through its blowhole at Sydney Harbor.

Marlin and Dory continue to search the harbor, both tired from looking at boats all night, when they are scooped up in the beak of a pelican. The pelican lands on a nearby dock and swallows them but Marlin refuses to have come this far just to be breakfast. He lodges himself and Dory in the pelican's neck, causing it to start choking. Nearby, Nigel wakes from a nap to notice the pelican, Jerry, choking and flies down to assist. He hits Jerry in the back, expelling Marlin and Dory from his mouth onto the dock where Marlin shouts out that he needs to find Nemo.

Nigel sees that he and Dory have flopped their way towards the end of the dock. Nigel chases after them but they are all forced to freeze when they notice that they are surrounded by hungry seagulls. When Nigel tells Marlin that he knows his son, Nemo, Marlin flips in excitement, causing the seagulls to rush forward, but Nigel manages to take Dory and Marlin in his mouth and fly off.

The dentist has installed a new high-tech filter, foiling the Tank Gang's escape. The dentist suddenly pulls Nemo up in a fish net but Gill and the other fish swim into it and instruct Nemo to swim down, pulling the net into the tank and away from the dentist's grip. Despite their efforts, Nemo is quickly scooped up in a plastic bag and set on the counter. Darla arrives, but Nemo plays dead to save himself. The other fish quickly realize that Nemo is feigning death so that he can be flushed down the toilet, but the dentist moves towards the trash can just as Nigel arrives in the window.

Nigel causes a disturbance, terrifying Darla and throwing the office into chaos. Marlin, seeing Nemo's act, believes Nemo is dead. After the dentist throws Nigel out (along with Marlin and Dory), Gill helps Nemo escape through a drain that leads to the ocean.

Nemo travels down the piping until he reaches a water treatment filtration, a series of piping that travels on the sea floor out of the harbor. Nigel flies out of the harbor with Marlin and Dory and releases them into the water, offering his condolences.

Despondent, Marlin bids farewell to Dory and begins his journey home. Marlin's departure causes Dory to lose her memory. Nemo emerges from the piping and calls out for his father. He finds Dory swimming confusedly under a buoy, saying that she's lost someone but can't remember. Nemo offers to search with her and Dory happily complies, though she doesn't recognize him. As they swim together, Dory comes upon a piece of piping and reads 'Sydney' on it. Suddenly, all of her memories come flooding back to her and she rushes at Nemo, hugging him fiercely, before leading him in the direction Marlin went.

Dory reunites Nemo with Marlin, but a fishing trawler captures her in a net along with a school of grouper. Though Marlin fears for Nemo's safety, he lets go and allows Nemo to do what he can. Marlin instructs the panicked fish from outside the net and they all soon start swimming in sync downwards, pulling the net with them until it finally snaps away from the boat, freeing all the fish. Marlin and Dory find Nemo under the heavy netting -- Marlin is stricken with grief, believing Nemo is dead. Nemo regains consciousness & Marlin gently tells him that he found out that sea turtles live to be 150 years old.

Marlin and Nemo come to an understanding and all three go back to their home in the reef. Marlin's demeanor has changed for the better and he is more upbeat and confident in his son's abilities. He takes him to school where Dory is dropped off by Bruce, Anchor, and Chum who have included Dory in their vegetarian program. Nemo hugs his father before heading off on another field trip with Mr. Ray. Marlin watches them leave, knowing that his son will be all right.

Back at the dental office in Sydney, the dentist curses the high-tech filter which has suddenly stopped working. He complains about having to put all the fish in baggies but notices that they have mysteriously disappeared from the counter. Horns honk out the open window as Peach is the last to cross the street and land herself in the harbor with the other fish. As they float in their baggies, unable to escape confinement, Bloat wonders what to do next.

The tiny fish that was Chum's "friend" at the support group is stalked by the angler-fish. As the angler-fish moves in to swallow him, the tiny fish suddenly opens his mouth to a surprisingly enormous size and swallows the angler.