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!"
( ‣ ) Associated production music
( • ) Original music
( ◦ ) SpongeBob music
• ? - Michael Bolger, Nicolas Carr, Pat Irwin [title card] ‣Arizona Fanfare - Jack Shaindlin [TV show] • ? - Michael Bolger, Nicolas Carr, Pat Irwin [SpongeBob, Patrick going over checklist] ‣Arizona Fanfare - Jack Shaindlin [Mermaid Man watch] ‣Crime & Danger Sign No. 3 - Hans Conzelmann, Delle Haensch [start of marathon] ‣ ? ["And now, without further fanfare..."] ‣Excited Chase 1 - Phillip Green [pineapple blows away] ‣ ? [Squidward watching ballet] ‣Excited Chase 1 - Phillip Green [Squidward's house blows away] ‣ ? ["Hey, that's it!"] • ? - Jeremy Wakefield [Squidward blows away] ‣Against All Odds - Paul Lawler ["We have found the Mermalair!"] ‣Fall to the Death - Harry Lubin [SpongeBob and Patrick fall into a net] • ? - Nicolas Carr ["Again!"] • ? - Pat Irwin [SpongeBob, Patrick laughing] ‣ ? ["In the beginning it was all dark."] ‣ ? [young Mermaid Man surfing] ‣ ? [Mermaid Man falls asleep] ‣Dramatic Bridge 4 - Phillip Green ["A wave drew me back into the ocean."] ‣Rainbow Delights - Jane Antonia Cornish ["I was rescued by mermaids!"] • ? - Jeremy Wakefield [Mermaid Man snoring] ‣ ? ["There I was in the ocean."] ‣Mount Olympus - Paddy Kingsland ["I had no other humans to talk to."] •Botany Bay - Michael Bolger, Nicolas Carr [Mermaid Man sees a ship] ‣Masked Crusader 2 - Harry Bluestone, Emil Cadkin ["A boy in trouble!"] ‣Master of Menace 2 - Harry Bluestone, Emil Cadkin ["Fear not, young man."] • ? - Jeremy Wakefield ["No, no, no."] ‣Arizona Fanfare - Jack Shaindlin ["Mermaid Man and Barnacle Boy!"] • ? - Michael Bolger, Nicolas Carr, Pat Irwin [bank robbery] ‣Heroes Salute - Harry Bluestone ["Thank you, sir."] • ? - Michael Bolger, Nicolas Carr, Pat Irwin [Barnacle Boy defeats Man Ray] • ? - Jeremy Wakefield [Mermaid Man orders a pizza] ‣Arizona Fanfare - Jack Shaindlin [TV comes back on] ‣Sprightly Link 6 - Harry Bluestone [Winchell Apartments exterior] ‣The Bachelor Life (a) - Laurie Johnson ["Come on, Ernie, the movie's about to start."] ‣Lost in the Galaxy - Harry Lubin [scientist doing tests] ‣Battle Zone - Harry Bluestone, Emil Cadkin [Ernie and Tim fall out of their apartment] ‣The Bachelor Life (a) - Laurie Johnson [movie night] ‣Imminent 4 - Harry Bluestone, Emil Cadkin [reaction to overcooked popcorn] • ? - Michael Bolger, Nicolas Carr, Pat Irwin [Ernie, Tim become Mermaid Man, Barnacle Boy] • ? - Jeremy Wakefield ["Ah, feels just like yesterday, doesn't it?"] •Slide Whistle Song - Nicolas Carr, Sage Guyton, Jeremy Wakefield [ending]
8:00 pm - The Mermaid Man and Barnacle Boy Marathon begins
February 29 - Mermaid Man and Barnacle Boy become superheroes.
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 episode's title is a parody of the 2005 Christopher Nolan movies Batman Begins.
The wind blowing SpongeBob's house and Squidward's house is an allusion to the 1996 film Twister.
In the book, 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.