Molly and Gil bring a comic book to school: 'The Super Adventures of Guppy Girl and Bubble Boy!', which Mr. Grouper reads to the class. The kids are excited and want to know all about superheroes.
As Molly tries to introduce the show, Gil zooms in wearing full superhero attire, complete with mask and cape! Molly asks the viewers what Gil is pretending to be as he continues to fly around and hum his superhero theme tune. To demonstrate his 'super strength', Gil lifts a huge cardboard skyscraper, only for Bubble Puppy to enter and rest on the top it, causing the building to crash to the floor. Molly asks if Gil is OK, to which he replies: "It's time for Bubble Guppies!"
The episode begins with Molly, who meets Gil and Bubble Puppy at a comic book store. Gil shows Molly a comic he found called 'The Super Adventures of Guppy Girl and Bubble Boy!', with Bubble Boy being Guppy Girl's sidekick. Molly asks what a sidekick is, to which Nonny explains as he leaves the store with his own comic books. As Gil tells Molly more about superheroes, they meet Justin, who works at the store. Justin shows Molly and Gil another comic book, about evil Sid Fishy, which he gives them to take. Molly and Gil thank him and continue excitedly to school.
When they get there, Gil and Molly show everyone their comic book and tell them about Guppy Girl and Bubble Boy. Mr. Grouper then gets everyone thinking about superheroes, including what they wear and what superpowers they could have. This inspires the guppies to sing a pop song about being superheroes!
After the song, Goby decides that he wants to be a superhero, and visits Deema's 'Superhero Superstore'. Goby tells Deema that he wants to be super strong, and steps into the super shower of power! There are three superpowers to choose from, and Deema asks the viewers to help her choose the right one. After choosing super strength over speed and flight, Goby exits the shower and lifts it, along with Deema, over his head! Mr. Grouper then announces that it's lunchtime.
Molly tells the viewers that superheroes can have all sorts of super powers, during which Gil flies in excitedly to tell her that Mr. Grouper is about to read the comic book to the class. Molly invites the viewer to come along too. Everyone gathers around Mr. Grouper as he begins reading The Adventures of Guppy Girl and Bubble Boy!
In Big Bubble City, Sid Fishy (voiced by Ozzy Osborne) is busy stealing the stinkiest smells in the whole city! The entire police squad (lead by Oona and Nonny) arrive to stop Sid, only to be blasted with stink sauce! This is reported by Goby on the news and confirmed to the mayor (played by Molly) by Deema. Meanwhile, high up inside his blimp, Sid Fishy reveals his plan to cover the entire city with stink sauce! With the police department defeated, Deema decides to call Guppy Girl. The Mayor, however, is Guppy Girl in disguise! Molly whispers to the viewers that she can't turn into Guppy Girl in front of anyone. With Guppy Girl not answering, Oona suggests that Deema calls Bubble Boy instead.
Bubble Boy (Played by Gil) answers the call, and Molly arranges to meet up and stop Sid Fishy. Molly then distracts Oona, Nonny and Deema long enough to change into Guppy Girl and fly away unnoticed. Meanwhile, Sid begins to fill an enormous cloud with stink sauce, intending it to rain all over Bubble City. Molly and Gil find Sid Fishy, but are spotted by Roughy, Sid's henchman, and are shot at with stink sauce. Not being able to get close enough, Molly tells Gil to distract Sid while she removes the pipe from the cloud. The plan almost works, but Molly is spotted by Roughy and is shot out of the sky. Gil sneaks on board and tries to turn off the machine from the inside, but is captured by Sid.
Molly distracts Sid with a cardboard cut-out of herself, and frees Gil, allowing him to trap Sid and his henchman inside a super bubble. After turning off the machine and destroying the blimp, Molly and Gil throw Sid and Roughy in jail. Sid explains to everyone that no one wants to be around him because of his smell, and that if he made the whole city stink, people might want to be his friend. Roughy tells Sid that he's his friend and, after a super bubble bath, both them and officers Oona and Nonny are squeaky clean! Deema then rushes in and tells everyone that she can't find the mayor anywhere, prompting Molly to wink at the audience. Everyone laughs as the comic book closes and the story ends.