The episode starts with a narrator explaining the situation at hand, also explaining that Daten City lies on the fault line between Heaven and Hell. He also says darkness is consuming the city, and that it is the angels' job to keep things clean and tidy.
The setting changes to that of a church, where Chuck is seen jumping around. He is suddenly struck by lighting, and spits out a note, which reads "WC". An alarm sounds, calling for both Panty and Stocking. They fall across the ceiling and land in front of Garterbelt, who tells them they've been blessed with a clue to solve a mystery. He proceeds to explain that some people were being swallowed by toilets, stating that it had to be a ghost's doing.
Panty and Stocking argue about Panty's sex life, before being told by Garterbelt that they need to keep collecting Heaven Coins in order to be accepted back in Heaven. Panty and Stocking go off in See Through to investigate. After driving around, they find a plumber, and believe him to be the ghost in disguise. Panty tackles him to the ground and shoots him, but since her gun can't hurt humans nothing happens. Panty says the plumber is actually kind of 'cute' and proceeds to have sex with him at a motel.
Panty and Stocking come back to Garterbelt, who is enraged, saying they never take their missions seriously. Garterbelt yells they should have dinner. After eating Garterbelt's curry, Panty went to the bathroom. The toilet swallows Panty up, and causes an explosion which covers the entire second floor in feces. Panty, completely covered in feces, says she now knows what's really going on, and wants revenge.
Giant Brown comes out of the sewers and proceeds to cover the entire city in feces. Some policemen arrive at the scene and try shooting the ghost, but it is unaffected. Garterbelt tells them that it's no use, explaining ghosts can only be defeated by angels. Panty and Stocking transform their clothing into a gun and a katana respectively, and kill the ghost easily, who explodes and leaves a Heaven Coin behind. Garterbelt assures their job is done, saying that the angels need to be punished, and they all go back to the church.