Tom and Jerry and their friends are invited to see the Mermouse and other mermice to race in the Annual Dolphin Race in the Lost City of Atlantis. As they finally arrived at the dolphin stables, they meet the Mermouse brushing a beautiful dolphin with blue swirly patterns on her whole body and is named Swirl. Mermouse sees them and swims over to shake hands with Sugar Belle, White Tabby, Tyke, Dripple, Clyde, Tim, Bernie, Mary Lou, and Cindy-Lou. But even though she is happy to meet some of Tom and Jerry's friends, she is still feeling nervous about the race because she has been looking forward to winning this year. Luckily, Jerry calms and soothes her and tells the Mermouse that she will win if she doesn't worry so much.
Just then, Tyke's stomach starts to rumble and the gang decides to go to the snack bar for lunch. The Mermouse says goodbye to Swirl and joins her friends to grab a bite. At the snack bar, the Mermouse explains that the winner who crosses the finish line first receives the grand prizes; a year supply of chocolate covered sand dollar cookies, a blue ribbon, and a golden trophy. She imagines Swirl with a blue ribbon on her and holding the trophy, hearing the crowd cheer. All this daydreaming was almost making it hard for the Mermouse to finish her salad. Tom took a bite out of his tuna sandwich and suggests that she and Swirl should practice so they can get better at winning the race for sure. The Mermouse likes that idea because the race is only 4 days away.
After they finished eating their lunch, the gang swam quickly back to the stables to see Swirl again. But when they arrived, they saw that Swirl's stable was empty. Feeling a wave of panic that hit her, the Mermouse began to shake a lot but Tim calmed her down and promised her that they will find her dolphin friend before the race. Just then, Cindy-Lou spotted a mess of tuna scraps on the sandy floor and a clue. It was a piece of purple cloth. Dripple picked it up, and examined it with a magnifying glass. The gang doesn't know where this piece of cloth came for. But what they do know is that they need to find the dolphinnapper with the initials G.G. and save Swirl.
Mermouse decides to join them because she knows how much she loves and cares for her dolphin. The gang followed Dripple, still holding his magnifying glass while looking at the tuna trail. Just then, the trail stopped at a coral wall. Mermouse sat down on a rock, wailing that they will never find Swirl. Just then, the rock pushed down and the coral wall opened. It was a tunnel that lead to the other side of the reef, and then Tom took out his flashlight just so everyone could see in the dark.
As they finally made it to the end, they discover a black coral castle with blue diamonds al over it. They swim into the entrance when suddenly, Cindy-Lou heard a melodious but hypnotic melody that got her into a trance. Tyke snapped her out of it by plugging her ears with earplugs and she was back to her old self again. Then he handed everyone else some earplugs too just so they wouldn't be hypnotized by the music that was come from the throne room. Bernie quietly flew in and perched on a bar just to see an ugly octopus with six arms holding whips while playing a yellow golden flute with two arms. He was using both the music and the whips to force the hypnotized dolphins, including Swirl, to work. They knew they had to save her. Tim pulled out the wishing sapphire and made a wish that they can become dolphins as well.
As the spell worked its magic, the gang became dolphins with different colors. They swam with all their dolphin might just to get closer to what the octopus was saying after he was done playing his music. After they removed their earplugs on, they could hear that the octopus' name was Gilburt Gills and that he is using the dolphins just so he can find the rarest golden pearls in the sea. Mermouse knew that Swirl and the other dolphins were in need of her and her friends help, but they must find a way to release them and fast before the race. Clyde pointed to a chain with a key around Gilburt's neck that might fit in the locks of the dolphins' cuffs and Tyke's brain hatches an idea. Tom and Jerry can distract Gilburt by entertaining him because they are the best performers, while Clyde and Mary Lou tries to get the key from his chain necklace,toss it to Mermouse,and release Swirl and the rest of the dolphins, then Sugar Belle, Cindy-Lou, White Tabby, and Bernie can make an escape route that will take them to Atlantis. But then Tim asks ”What about the flute, Tyke? How are we suppose to get it without being hypnotized?” when Tyke suggests that he and Tim should wear their earplugs. While Tom and Jerry are doing the entertaining, they can snatch the flute and snap it in two.
As Gilburt sat on his throne, he was surprised when Tom and Jerry came in with beach balls, hoops, and other cool stuff. Tom balanced a beach ball on his dolphin snout while Jerry whirled a hula hoop around his brown dolphin waist. Gilburt seemed to be enjoying this, and Tyke's plan was working perfectly just as he hoped it would. He signaled Clyde and Mary Lou to quietly sneak up and snatch the key out of the chain. Mary Lou worked her paws and carefully unchained the necklace and Clyde slipped the key out with his big but gentle dolphin flippers. Then Tyke and Tim swam in next and quietly snatch the flute out of Gilburt's tentacle, but before they can swim away, Jerry accidentally sent the beach ball flying and it lands on Tim's head and he shouted "OUCH!" then clapped his mouth shut. Gilburt snapped right back out of the zone and saw the kids with the key and his flute. Angered and realizing that he had been tricked, he swam straight toward Clyde and Mary Lou and Tim and Tyke to get his key and flute back, but luckily Tom and Jerry defended them by slapping his face with their dolphin tails and gave them time to get to the pink coral where the chained dolphins are being held prison.
As the finally arrived, Clyde quickly gave Mermouse the key and she swam to one dolphin and the next, unlocking their cuffs that was hurting their necks. After the last dolphin was free and swam to where the escape route was, she swam to her dolphin friend, Swirl who was suffering from the cuff around his neck and the scarsand bruises that the whips have made. Mermouse calmed her down and gently put the key in the keyhole, setting Swirl free.
Just then, they heard an "Incoming!" coming from they castle doors and came out Tom, Jerry, Clyde, Mary Lou, Tim, and Tyke who were swimming as fast as they could to get away from Gilburt who was chasing them. He was still trying to get his flute back from them, but they were too fast for him since they have dolphin powers. Mermouse lead them to the escape route where Sugar Belle, White Tabby, Bernie, and Cindy-Lou have finished making. Mermouse hoped on Swirl, but she was too hurt to swim fast enough. Just then, Tom and Jerry swam along and helped her up while Mermouse took her under. They made it to the escape route but as they were about to jump down, Gilburt appeared behind them and ordered them to give him his flute back. Tim swam over and held his paw out with the flute in it. Tom begs his twin brother to not give it to him because he might hypnotize them again. But Tim winked at Tom and he smiled trustingly. As Tim gave the flute to Gilburt, he began to play but instead of a hypnotic melody coming out, a disgusting,noisy sound came out making the others cover their ears. Gilburt soon realized that this isn't his real flute and has been tricked again. Tim pulled out the real flute and snapped it in two which cause Gilburt to wail. The gang quickly swam to the escape route just in time before he can catch up with them.
As they finally made it to Atlantis, Cindy Lou looked at the scars and bruises then putted some special ointment and bandaged them up. She said that the ointment will heal them for 4 days before the race. On Day 2, Swirl's bruises were feeling a little better and less painful when Mermouse rode on her for practice. After she jumped through the last hoop, the gang cheered and Jerry swam over to them then said that they'll do great in the race tomorrow.
The next day, Swirl was finally healed and the racers were ready to start. As the stoplight turned green, them and their dolphins were off. The kids cheered as hard as they can,and Swirl caught up with the other racers as she passed by them. There was an obstacle course at the other side of the race and Swirl dodged through big rocks while Mermouse held on for dear life. Then, the racers came to the hoops. The first one got through two out of three hoops, the other got all tangled up with his partner, but Mermouse and Swirl got through them in a perfect line. Jerry crossed his fingers and bit his lip as the two of them crossed the finish line and the crowd cheered.
Mermouse held the trophy and Swirl admired her blue ribbon on her cheek. Jerry and his friends congratulated her and the paparazzi snapped their photo. After the race, Mermouse gives her friends some tasty chocolate covered sand dollar cookies and tossed one to Swirl who jumped up and gobbled it up in recorded time, and the gang laughed.