The music video for "Happiness in Slavery", directed by Jon Reiss, was inspired by the 1899 novel The Torture Garden by French author Octave Mirbeau. It features performance artist Bob Flanagan entering a large room, placing a flower and a candle on an altar and in a ritualistic style prepares for something; by stripping naked and washing himself before becoming strapped into a machine with long robotic claws that arise from the machine and subsequently tear apart his skin and impale his hands. The man reacts with pleasure as this occurs. There are also drills that drill into his skin in various places letting his blood drip onto the floor beneath, where there is a garden apparently being fertilized by human blood.
Later in the video, large grinders emerge from the machine to cause extreme injury to the man's skin. As he continues to scream in a mixture of pleasure and pain, the machine begins to disembowel him, ultimately killing him. It then engulfs the man's body in a metal cask and minces it into fertilizer for the garden below. In the conclusion, Trent Reznor, who had been singing the lyrics inside a cell at the beginning of the video, enters the room and performs the same ritual that the previous man performed, but is unseen.
The video was almost universally banned once released, but was later included on the Closure video album and in the Broken film. It was featured on Too Much 4 Much, MuchMusic's showcase of videos banned from their regular programming.
Reznor commented that the video was not created for shock value, but because "these were the most appropriate visuals for the song." It had to do with his artistic freedom at the time after his fallout with TVT Records.