An English-language version of the film, with Alan Rickman (Joe the Fish) and Terry Jones (the Professor) as voices, premiered at the beginning of April 2005 on the Latin American version of the Cartoon Network. It was available earlier in the UK.
Danish teen-pop girl-group, Little Trees performed the title track, "Help! I'm a Fish (I'm A Little Yellow Fish)", which was released as a single in the UK. Fellow Danish girl group, Creamy also recorded a version of the song.
A great white shark and a pilot fish come across the leaking bottle of antidote and gain the human characteristics of intelligence and speech by inhaling the liquid. Using his newfound gifts, the pilot fish, who now calls himself Joe, sets about creating an underwater civilisation of intelligent fish. They take residence in a sunken oil tanker and begin to transform it into a monument.
Fly, Chuck and Stella are reunited, along with a seahorse named Sasha, but are horrified to discover that the antidote has been lost. If they don't find it before tomorrow's sunset, they will stay fish forever. Some travelling fish tell them about Joe and his "magical potion". Thinking it must be the antidote they are looking for, the children travel to Joe's oil tanker empire.
At the tanker, Fly attempts to steal and drink the bottle of antidote, but is warned by Chuck that if they turn back into humans this far beneath the ocean, they'll die. Intrigued by this, Joe has the children arrested and demands they manufacture more of the antidote or he'll have them eaten by the Shark.
Meanwhile, Fly and Stella's parents, Lisa and Bill, arrive home to find Aunt Anna frantic with worry. They find that Fly's fishing equipment is gone, so they head to the beach to search. There they meet Professor MacKrill who, having survived the storm, explains that their children have been turned into fish. He and Bill head out to search for the children in a cobbled-together ship fitted with a large water pump.
The next morning, the children manage to escape with the help of Sasha. With no chance of going back to retrieve the bottle of antidote, they decide that their best hope is to find the ingredients to recreate the antidote themselves. Just as they complete the formula, they are discovered by Joe, the Shark and their army of crabs. During the standoff, Joe and the Shark get into a heated argument. Taking this opportunity to escape, the children are stopped by the leader of the crabs who seriously injures Fly and drinks the antidote himself. Just as the new "King Crab" and his army is about to capture the children yet again, a tremendous underwater twister, generated by the Professor's water pump ship, sucks all the villains to the surface.
Now alone, Fly injured, and with only twelve minutes until sundown, Chuck realises their last hope is to make it back to the Professor's lab where a whole jug of antidote is stored. Showing unexpected courage and determination, Chuck carries both Fly and Stella through the dangerous seawater intake pipes back to the lab. However, they are pursued by Joe who overpowers them and steals the antidote. While Chuck fights off the Professor's escaped piranhas, Fly manages to catch up to the fleeing Joe and tricks him into drinking enough antidote to become mostly human. Since Joe can no longer breathe underwater, he drowns.
Fly drags the jug of antidote back to the lab and collapses. Chuck uncorks the jug just as Lisa and Aunt Anna open the door to the laboratory, causing everyone to get swept away. As the water drains away, Chuck and Stella have become human once more and are reunited with their parents. After a few tense moments in which a stuffed fish is mistaken for the limp body of Fly, the human Fly emerges from one of the lab's pipes.