Two clown fish, Marlin and Coral, are in a grotto, excited about the many children they are about to have. They go into an anemone. A barracuda arrives and attacks the eggs, creating a current which slams Marlin against the anemone, leaving him unconscious. Marlin wakes up, finds only one egg left, and names it “Nemo.” An egg he didn’t find survives and ends up safely in another grotto along with a pile of Fighting Fire fish eggs.
Nemo goes to school, where the kids want him to once again tell them about his adventures in Sydney. Dory, whose memory is getting a bit better, goes out for a swim and finds a bottlenose dolphin named Percy, who is lost. She learns he was recently released from a boat by humans who work for Planet Blue, a large marine animal amusement park, and is being tracked via a transmitter on his dorsal fin.
Nemo and another young clownfish, Remy, come across each other and examine each other curiously. They mimic each others moves. Remy thinks Nemo is a long lost brother of his. Marlin arrives, sees Remy’s resemblance to Coral, and confirms that Remy is a long lost brother of Nemo. As Nemo and Remy get to know each other, they become competitive and try to one-up each other. Remy is stronger, but Nemo is smarter. They become jealous of each other.
It is Nemo and Remy's birthday. Marlin hosts a birthday party and seems to favor Remy’s idea of what game to play first. Nemo gets angry and swims off. Remy catches up and Nemo fights him. Marlin catches up and breaks up the fight. Remy gets angry and swims off. A boats propeller churns the water around the around the trio, confusing them. Percy speeds towards Remy while trying to escape a net coming from the boat. Remy can’t move because he is frozen in fear. Marlin pushes Remy aside but slams into Percy. The net captures Percy and Marlin and is lifted up into the boat, which speeds off.
Dory finds Nemo and Remy and they tell her what happened. Dory remembers that Percy is being tracked by Planet Blue. Dory, somehow being familiar with Planet Blue, knows where the boat is headed. She leads Nemo and Remy as they head off to where Planet Blue is located.
At Planet Blue, Marlin and Percy are put in a dolphin tank and the transmitter is removed from Percy’s fin. They see some dolphins performing in a show while others are preparing for it.
Dory, Nemo, and Remy arrive at the bay in Australia next to which Planet Blue is located. Remy finds a large intake pipe leading into the park. They get too close to it and are sucked in towards a motor. They manage to make it back out of the pipe with the help of a branch that lodged in it, temporally reducing the suction.
Dory finds an outflow pipe and suggests they try to swim through it. Nemo tries to swim into it, but the current going out the pipe is too strong. Determined to show off his strength to Remy, Nemo tries to make it through the pipe, gets too tired and collapses onto the seafloor. Gill finds Nemo and joins Remy and Dory to try to find a way into Planet Blue. They determine if they block the inflow pipe, they can safely get past the motor. They get sea lions to steal a parasail from humans and put in into the inflow pipe to block it. Gills shows them the dolphin tank on a laminated map of the park they found and tells Dory and the boys to go there.
Going into the pipe, they come across an intersection, but pick the wrong way and end up in an octopus tank. While Dory finds and looks at a map of Planet Blue, an octopus captures Nemo and Remy. Dory finds a squeaky toy and throws it at the closed tentacles, which release the boys. Nemo and Remy escape with Dory back into the pipe intersection. Dory, now knowing where the dolphin tank is, picks the pipe that leads to it.
Marlin tries to get the Percy and some other dolphins, Bette and Redgrave, to help him find a way back into the ocean, but they are enjoying being in the dolphin show. Percy gets the idea to use his tail to flip Marlin over the fence and into the ocean. Percy attempts this, but Marlin falls short into a bucket of water next to the fence. A janitor picks up the bucket and puts it on his cart to transport it.
Some divers inspect the blocked inflow pipe. Nemo, Remy, and Dory reach the dolphin tank and watch the dolphins finish their show. The janitor stops near a polar bear exhibit area and accidently tips over the bucket, sending Marlin into the exhibit’s pool. A polar bear named Blanca approaches Marlin and tries to eat him, but Marlin manages to befriend her.
The dolphins tell Dory, Nemo, and Remy that Marlin is in a bucket that was headed to a polar bear exhibit. Remy tries to leave the dolphin tank to look for polar bear exhibit, while Nemo tries to ask Redgrave for directions to it. While Dory tries to bring the two together, a trainer sees her and captures her with a net. Nemo and Remy chase after her, but another net chases them to the side of the pool.
Redgrave grabs the pole of the net chasing Nemo and Remy before flinging the trainer into the pool. Other dolphins do this to other trainers with other nets. Redgrave shows Nemo and Remy the way to the polar bear exhibit. Meanwhile the divers have managed to unblock the inflow pipe. Nemo and Remy go into the pipe, get caught up in the current, and end up trapped in a closed Pirate themed pool. They agree to split up to find an exit before meeting in the middle.
Two polar bears want to eat Marlin, whom Blanca is protecting. Blanca leads the two polar bears out of the pool to fight them. The two polar bears work together to push Blanca to the ground before returning to Marlin. Just as the two polar bears approach to eat Marlin, they are fed with more appetizing fish and abandon him.
Gill once again tries to get the sea lions to block the inflow pipe. They had covered it with a lawn chair but it is only partially effective. Gill tries to motivate the sea loins to keep helping instead of sunbathing.
In the Pirate themed exhibit Remy finds an exit and looks as if he about to escape. Nemo angrily sees this and punches Remy, who falls onto some rocks. Remy is humiliated and tries to flee from Nemo. Remy runs into a venomous sea snake, who tries to eat him. Nemo distracts the snake. The snake thinks it is seeing double and is confused. Remy and Nemo work together to confuse and tie up the snake before fleeing into the pipe. The snake untagles itself and chases them. Nemo and Remy end up in a tide pool exhibit. A net scoops Remy up, and Nemo joins him in the net. The two are transported into a small, barren aquarium. Thinking the fish are sick, the keeper adds antibiotic to the water. Remy's wound from the rocks gets infected and he develops a fever.
Gill has motivated the sea lions to steal enough items to once again to block the inflow pipe.
A polar bear keeper finds the inflow pipe is being blocked again, which heats up the pool of the exhibit. The keeper sees Blanca trying to pry open a blocked outflow pipe for Marlin and thinks this is because the water is getting too warm. They add snow to the tank to cool it, which makes Marlin start to freeze.
Remy’s wound has healed. Nemo and Remy are scooped up by a keeper in a plastic bag. They are transported to a large coral reef exhibit, where they find Dory, who has found her many siblings from her childhood. They find an outflow pipe, but a diver seals it up for maintenance. Nemo, Remy, and Dory find the main outflow pipe. They see a worker emptying protein skimmers into it. They get into the protein skimmer, which is emptied into the outflow pipe.
Marlin is slowly freezing to death but Blanca is trying to keep him warm. Blanca, seeing Marlin needs to escape, finds a bucket, fills it with water, and puts Marlin in it. Blanca climbs the back wall with the bucket onto a catwalk. The polar bear keepers see them escape. Blanca goes down a ladder with the bucket into a service area. Blanca falls off the ladder and through a security gate, still holding onto the bucket with Marlin in it. Blanca runs freely through the amusement park. The polar bear keepers chase them with tranquilizer guns. Blanca is shot, but is able to go far enough to transport Marlin to a marshy landscaping pond.
A diver is about to unblock the inflow pipe when a great white shark named Bruce arrives and scares him way.
An engineer determines the solution to the blocked inflow pipe is to block the outflow pipe in order to create enough water pressure to unclog the inflow pipe.
Dory, Nemo, and Remy find Marlin in the marshy landscaping pond. Remy sees Marlin and Nemo embrace and gets upset, but Marlin and Nemo reassure him that he is part of their family. Dory finds the outflow pipe to the ocean. They go into it, but see that the outflow pipe is being blocked. They make it out just in time to avoid being trapped, but Dory hits her head on a root and is knocked out. Meanwhile, the inflow pipe is unblocked by the outward water pressure.
Dory wakes up, no longer having memory problems of any kind. Dory remembers how she escaped into the ocean. Dory leads Marlin, Nemo and Remy through the pond to a water wheel, which rises up next to a log flume track. They jump into the waterwheel, up onto the log flume track and down into a splashdown lagoon at the bottom of a big drop. Near the track, they wait for a log to pass by, which creates a splash that accelerates the four over the border fence and into a fast moving tidal river, which empties into the bay. They find each other and celebrate. Gill and the sea lions wave as Nemo, Remy, Marlin, and Dory head off for home.
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