"Wool" begins with a man awaiting his execution. The man is Holston, a sheriff of an underground silo bunker that contains the descendants of humans who survived the apocalypse. The silo shelters its residents from the earth's toxic surface, which they view through a projection on a blurred screen.
Jumping back three years in time, we follow Holston's wife, Allison, as she discovers overwritten files documenting several "uprisings" carried out over the centuries. Allison begins to speak out against the regime in the silo, suggesting that perhaps the silo's leaders wiped the files to keep residents from wanting to go outside. Allison also suspects that the image on the screen is fake and that the earth's surface might be habitable.
Holston dissuades Allison from sharing her theories, as her ideas might get her sent to "cleaning," a form of capital punishment where criminals go to the earth's surface to clean the camera lenses capturing the view. Holston and Allison both struggle to understand why the condemned always carry out the cleaning, which only benefits those who condemned them.
Fully convinced the surface is habitable, Allison feigns a psychotic episode, screaming that she wants to go outside. To say this is to commit "the great offense"—a capital offense. Allison is sentenced to cleaning, and as she awaits her punishment, she tells Holston that she will return for him. Holston waits three years before finally deciding to undergo the cleaning himself.
In the present, Holston discusses the nature of the cleaning with Mayor Jahns before willingly going to his death. He is fitted for his suit and receives an explanation of the cleaning procedure before he is released through the airlock. Holston walks to the earth's surface and is delighted and shocked to discover the world is habitable, with green grass, blue skies, and intact buildings. Pitying the "inside people" living in the silo, he conducts the cleaning before climbing a distant hill to find Allison.
Soon after, however, Holston begins to suffocate, believing the technicians only gave him enough oxygen to survive through the cleaning. He grabs a rock and forcibly removes his helmet. As soon as his eyes adjust, he realizes that the earth's surface is the same wasteland as projected on the screen in the silo, and his visor is actually a screen displaying a false image of a green landscape. Crushed and dying, Holston holds Allison's corpse and wonders what the people inside the silo see.
