Panty and Stocking are sent to investigate several cases of people getting eaten by toilets, which are caused by a ghost bent on covering Daten City in feces.

While investigating a series of disappearances at Daten City High School, Panty and Stocking encounter Queen Barby, the cheerleading team captain whose reign as the most popular student is threatened by the Anarchy sisters. With the help of the teenage occult geek Brief, Panty and Stocking expose Barby as the Ghost behind the school's disappearances.

Panty and Stocking get into a heated argument over a missing cup of pudding and go their separate ways. However, they are forced to put their differences aside to defeat a pair of Ghosts who work as a team.

Stocking finds herself gaining weight and goes on an intense diet, but she only keeps getting fatter until she balloons into a giant. When the cause is revealed to be from an obese Ghost who refuses to diet, Stocking sets out for revenge. Upon defeating the Ghost, Stocking returns to her original figure.

A recreational nose-picking fad spreads across Daten City thanks to a man named Oscar H. Genius, who invites the citizens of Daten City to a blimp party. However, Genius turns out to be a Ghost intent on ramming the blimp into the moon using the passengers' collective nosebleeds.

Panty and Stocking arrive at school to find that a strict academic regime has been established by the mayor's daughters, the Demon sisters Scanty and Kneesocks, and are banished to the lowest class in school. Together with Brief, Panty and Stocking discover that Scanty and Kneesocks are demons who are running a factory that produces an army of fake Ghosts beneath the school. A destructive battle ensues, with the Anarchy sisters defeating the Daemon sisters by destroying the stone that powers the factory.

Panty and Stocking's sibling feud escalates into all-out war when they eat the cores of two warring alien robots and transform into robots themselves. When the alien robots decide to join forces to destroy the human race and merge into a Ghost, Panty and Stocking are once again forced to work together to defeat the Ghost.

Daten City High School holds a lingerie run in which participants must race in their underwear. The run is interrupted by a Ghost who eats underwear, including Panty and Stocking's weapons, so Panty must resort to using whatever underwear she can find.

Panty and Stocking once again face off against Scanty and Kneesocks, this time in a volleyball match to determine who will control the public beach. The Anarchy sisters win, but the Demon sisters unleash a horde of aquatic Ghosts to wreak havoc before making a getaway.

Panty and Stocking are shrunken down and wind up inside Brief's body where they wreak havoc.

Panty and Stocking suspect Garterbelt of engaging in sexual activities behind their backs and search for incriminating evidence to use against him. They instead find Garterbelt's diary, which details his past life as a crime lord before he was killed and forced by God to live through all of history until he agreed to become His missionary.

Scanty and Kneesocks report the results of their unsuccessful battles with Panty and Stocking, as well as the whereabouts of the blood kin of Hell's Monkey, to Corset, the mayor of Daten City.

Having lost her powers, Panty is kicked out by Garterbelt and moves onto a farm with an old woman who, unbeknownst to her, is in league with Garterbelt and persuades her to stop Corset from using Brief to unlock Hell's Gate. Panty has sex with Brief, losing her virginity and restoring her powers. Stocking returns to help Panty fight Corset and the Demon sisters.