One Saturday morning, SpongeBob is watching his favorite show, The Adventures of Mermaid Man and Barnacle Boy while eating Mermaid Man and Barnacle Boy Bran Flakes. He has entered a competition and is listening eagerly to see if he has won the mystery prize. The announcer declares the winner as "SpringBoob SquirePin," for his life-sized Krabby Patty mannequins of Mermaid Man and Barnacle Boy. SpongeBob calls out that "SpringBoob SquirePin" stole his idea before the announcer announces that he has made a "slight" error in pronunciation and that the real winner is indeed SpongeBob SquarePants.
Within seconds, SpongeBob's prize is delivered to him. SpongeBob has won the "Conch Signal," a conch whose noise is a signal which Mermaid Man and Barnacle Boy respond to. SpongeBob blows it, and Mermaid Man and Barnacle Boy hear it from Shady Shoals, and spring into action. When they arrive at SpongeBob's house, they at first think that he has been disfigured before recognizing him. He explains to them that he won the Conch Signal in a contest and that there is no danger. They then explain to him the importance of the signal and tell him that he must only use it for major emergencies.
Later on, Mermaid Man and Barnacle Boy hear the conch once again and rush to SpongeBob's house, where he appears to be dead on the floor. However, he then reveals that he simply is having trouble opening a jar of mayonnaise. Barnacle Boy is angered by this, but Mermaid Man reminds him that emergencies do not come around as often as they used to, and he tells SpongeBob that he can blow the conch "every once in a while.". However, SpongeBob abuses this privilege, constantly calling Mermaid Man and Barnacle Boy to help with normal everyday tasks. Eventually, the two heroes are exhausted, and Barnacle Boy attempts to destroy the conch signal, but cannot bring himself to do so.
SpongeBob is in tears and apologizes, explaining that he just wanted to spend time with them and Mermaid Man tells him that the conch signal isn't good for him. As a result, they let SpongeBob join them on their daily patrol, with SpongeBob dressed as a superhero. They do various activities, such as keeping lookout from on top of a tall building, and in the street, Mermaid Man and Barnacle Boy see an old man, who was once the Atomic Flounder. SpongeBob attacks the old man, not understanding that he is no longer a villain, and angered by this, the Atomic Flounder breathes fire in Barnacle Boy's face.
At a restaurant, Mermaid Man and Barnacle Boy ask SpongeBob to find their theme song on a jukebox. As he tries to find it, they decide to "ditch" SpongeBob. Outside, however, they are attacked and trapped by their nemesis, the Dirty Bubble. When SpongeBob finally finds the song, he comes outside to tell them and sees their predicament. He asks the Dirty Bubble for his autograph, saying that he is his favorite supervillain, and "accidentally" pops the Dirty Bubble with the tip of the pencil, saving the day. The trio rides off in the Invisible Boatmobile, singing a Mermaid Man and Barnacle Boy-themed version of "Jingle Bells" as the episode ends.
This is the only Mermaid Man and Barnacle Boy episode where the title card has purple scales. The other four have blue scales on the title card, and "Mermaid Man & Barnacle Boy VI: The Motion Picture" has a completely different title card than the others.
When Barnacle Boy's head explodes after it got burned by The Atomic Flounder's breath, his face resembles the Muppet, The Great Gonzo.
When Mermaid Man tells SpongeBob that the conch signal is too much responsibility, the television in his house shows only a red screen, instead of a black screen or a moving picture.
When Mermaid Man says "Activate torpedo mode!," the regular closed-captioning just says "Torpedo mode!"
Towards the end of the episode when SpongeBob, Mermaid Man, and Barnacle Boy are singing the "Jingle Bells" parody, Barnacle Boy's mouth does not move when they turn past the rock, even though he is singing.