The episode begins at SpongeBob's house, and SpongeBob and Patrick are preparing for a Mermaid Man and Barnacle Boy television marathon. As the first show, an "Origin Special", begins, SpongeBob's house loses power and then a wind rips the house and TV away. SpongeBob and Patrick go to Squidward's house, but the wind follows them there and destroys his house, too. SpongeBob and Patrick go to the Mermalair to ask the heroes about their origin in person.
Mermaid Man goes on a flashback, but it wasn't the actual story of his origin. Then, he tells another flashback, this time it is the origin story. In this flashback, Mermaid Man encounters mermaids while he is drowning that let him breathe underwater with the sea star on his nose.
Then Mermaid Man tells a flashback where he finds a drowning Barnacle Boy and saves him. They then become partners, partly because Barnacle Boy was stuck breathing underwater for the rest of his life as a result of the rescue. They stop a bank robber in the next flashback, then thwart Man Ray in the next, but the two argue over the legitimacy of the flashbacks.
Then, the "actual" origin episode starts to air on the Mermalair's giant monitor, in which Mermaid Man (called Ernie in the story) and Barnacle Boy (called Tim in the story) are roommates. The following "origin episode" didn't make sense because of how random it was (see transcript for details). After cooking popcorn for movie night, they are thrust into an improbable series of events, and eventually return to their apartment. The now overcooked popcorn causes a radioactive effect on the two, giving them superpowers and the urge to fight crime underwater. They dive into the sea and start fighting crime. As the show ends, Mermaid Man and Barnacle Boy were baffled. Finally, the camera cuts to SpongeBob and Patrick putting popcorn into a microwave with intent to overcook it and give themselves powers. The episode then ends with Mermaid Man and Barnacle Boy yelling "No!"
Tim Conway voices Barnacle Boy, and in this episode, Barnacle Boy's incorrect real name is Tim. His real name has already been confirmed as Kyle in "Mermaid Man and Barnacle Boy V". Ernest Borgnine plays as Mermaid Man, and Mermaid Man's name is really Ernie (which is a nod to Borgnine).
The wind blowing SpongeBob's house and Squidward's house is an allusion to the 1996 film Twister.
In the comic book in "Ditchin'" they were brothers, and were born from superheroes. In earlier episodes, however, it was said that Barnacle Boy was Mermaid Man's son. It was also said that they got their powers from King Neptune.
It is unknown which story is actually true.
This is the first time in the series that humans above water are portrayed as typical cartoons and not in live action. Also, in this episode, Bikini Bottom looks bigger than in other episodes despite the fact that SpongeBob and Patrick were smaller than the sea artist's pencil in "Frankendoodle" and much smaller that that of David Hasselhoff in the movie.
In this episode, the mermaids faces are drawn realistically.
Mermaid Man finding Barnacle Boy and rescuing him from drowning by giving him his abilities is a parody of how Birdman met Bird Boy (the only survivor of a shipwreck) and gave him his abilities.
This is the first episode to mention telekinesis.
Ernie is first bitten by a radioactively infected specimen of ant in "the apartment directly above", but when the two are flung back into their apartment, their window is shown to be on the top floor.
This was Ernest Borgnine's last episode to make, that aired before his death on July 8, 2012. There were several episodes that had Mermaid Man in them, after Ernest's death.
The radioactive bug biting Ernie's forehead is a reference to Peter Parker (Spider-man) getting bitten by a radioactive spider from Spider-Man.