A cutout of him appeared in the Mermaid Man and Barnacle Boy TV show as a cutout at the start. When SpongeBob was with Mermaid Man and Barnacle Boy, they saw the Atomic Flounder who was revealed to be retired. SpongeBob then attacks him on the account that he's a super villain. Enraged, the Atomic Flounder used fire breath to burn Barnacle Boy's head.
He, alongside many other villains formed a book club even though Mermaid Man and Barnacle Boy thought they were up to no good. However, it was revealed at the end that all they did was form a book club.
After SpongeBob, Barnacle Boy, and Patrick think that Mermaid Man has been kidnapped, they go to Atomic Flounder's Home, where they find Man Ray proposing a scheme to rob a bank. While looking for Mermaid Man, SpongeBob cuts through the bank map because he thinks there is a secret pass way behind it, but there is not. The Atomic Flounder tells SpongeBob that Mermaid Man is not there, so the three continue to search elsewhere. Later, at Jumbo Shrimp's House, the Atomic Flounder, Man Ray, and the Dirty Bubble come over. Here, they have a meal and then complain about how SpongeBob, Patrick, and Barnacle Boy have ruined their day. They all agree to get their revenge on the three. Later, they kidnap the three and tie them up to chairs at Jumbo Shrimp's house. Soon, Mermaid Man arrives to give Barnacle Boy a present because it is his birthday, but he gets tied up too. Soon, it is time for the villains to get their revenge. Barnacle Boy has an idea. He asks SpongeBob and Patrick to sing him a birthday song while he plays the harmonica he just got as a present. They do so and this causes the villains to get annoyed and they kick the heroes out.
The Atomic Flounder's atomic breath, which was seen in "Mermaid Man and Barnacle Boy II," is possibly a reference to Japanese film character Godzilla.
He was actually a fish in a lab experiment, but it went haywire and he became the villain he is now.