"The SpongeBob Pets" is the first episode of Season 4 of The Wonder Pets and a 44 minute crossover special.
Ollie makes a comic called "Bunny's Ideas" which is so nice, so he makes a schedule to have the Wonder Pets go on an air trip. after they get everything ready, they out of their home. When they fly into the sea to stop at a gas station, their flyboat is stolen, leaving them stranded outside Bikini Bottom. At the Brag-Mart, Spongebob introduces himself to the Wonder Pets and takes them to the Bikini Bottom Police Department, where they are turned away by the police fish since they did not contribute to the Policeman's Office.
The SpongeBob gang puts up the Wonder Pets in their home until things improve. Mr. Krabs shows the arch enemy, Evil Snake his slingshot, and teaches him how to make money, but is then found by Plankon, so Evil Snake takes revenge by kidnapping Plankton. Meanwhile Squidward tries to find something Tuck is good at, finds that he is a natural at the clarinet, but downplays his talent out of jealousy. Ming-Ming and Ollie help Patrick take Gary for a walk, with Ming-Ming trying to teach Gary independence, but he runs off when freed, leading them on a chase through town until he gets lost. Sandy notices Gary missing and Ming-Ming and Ollie try to fake his presence, but he eventually returns. SpongeBob and Linny try different plans to find the flyboat, each one backfiring, until they discover that the flyboat was taken by Plankton by mistake.
The two celebrate at Goo Lagoon, but things go bad when Linny tries to introduce Spongebob to hotdog palace and the ale is revealed to be a knock-off of Duff Beer. This results in the Blue Haired Lawyer filing a lawsuit against the Ice Cream Area for patent infringement with Linny forced to defend the brewery to save the home of the classroom as the brewery is the town's largest helper. CatDog is the helper who presides over the case. During the trial, similar characters from both shows interact with each other, including both shows' versions of Blue's Clues. Dog finds in favor of the dining restaurant, but declares that both sodas are imitations of his own favorite soda "Root Beer!".
The pets prepare to return to their home. Squidward gives Tuck his clarinet, but Ming-Ming throws it away, as there is no room for any more luggage. Evil Snake points out that he took revenge on all of Mr. Krabs' enemies; Mr. Krabs is sickened by this and bids him goodbye. Linny and SpongeBob try to explain their actions, and drive a boat and the two end up having a runaway car style all through Bikini Bottom, crashing into the Krusty Krab and the gang get rid of Plankton by sending him back to the Chum Bucket. Returning home, the Wonder Pets celebrate their rescue adventure.
- Spongebob's old voice similar to the one from "Hall Monitor" is used.