Throughout their career The Aquabats have maintained a fictitious backstory which purports them to be superheroes from a distant island called Aquabania. The band's costumes and pseudonyms tie into this mythology, which is detailed in the liner notes of their albums. Over the years the story of their origins has evolved, changed, and occasionally been reconnected to explain changes in the band's lineup. They have also built up a roster of allies and enemies, many of whom are featured in their album artwork and often appear onstage with them as costumed characters in choreographed fight scenes.

According to the most consistent elements of the band's mythology, the original 8 (or 9) members lived on a distant and idyllic island known as "Aquabania," populated by humanlike bat creatures. The island was attacked by the villain Space Monster 'M' and 8 (or 9) of its inhabitants fled to the ocean in a hollowed-out log. They washed ashore in California, where they were taken in by Professor Monty Corndog (portrayed onstage by singer Christian Jacobs' brother, Parker Jacobs), who used chemicals to revive them and give them super powers. They donned costumes including "radioactive rash guards," "power belts," and "anti-negativity helmets" (many of which are sold as part of the band's merchandise catalogue) and decided to channel their powers through music in order to "take over the world" by attracting legions of fans. This would then allow them to combat Space Monster "M" and retake their homeland.

Space Monster "M" placed a bounty on the heads of the Aquabats, attracting numerous villains and monsters to pursue and attack them in attempts to end their musical quest. These costumed villains often appear onstage to combat the band in concert. In addition to Space Monster "M," some of the more notable Aquabats enemies to appear over the years include Powdered Milk Man!,The Sandfleas, The Floating Eye of Death, The Cyclopsis, and Pumpkin Face. Along with their rogue's gallery, the band has also amassed a list of allies who assist them in various capacities. In addition to the Professor, some of the more notable Aquabats allies have included their former webmaster The Pigbat, The Sea Ghost, Danger Woman, and Digital Unicorn.

The band's superhero mythos has often been used as a device for explaining their numerous lineup changes. For example, members departing the group have sometimes been said to have been wounded in battle with the band's enemies, and when Jimmy the Robot joined, it was explained that the Professor constructed him out of various materials in order to provide the band with a robotic musical virtuoso.

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