My Prerogative was filmed at The Paramour Mansion in Silver Lake, Los Angeles, California and begins with Spears driving a Porsche 928 at high speed in the Hollywood Hills. She crashes through a fence and lands into a pool inside a manor where a party is taking place. She emerges from the water and crawls in top of the car to sing the first verse. Spears's brother Bryan makes a cameo in these scenes. After she leaves the pool, she enters the manor and passes couples making out around her. She appears in a stainless steel kitchen, where a maid cuts the straps of her black wet dress. In the next scene, she walks into a study in which her husband at the time, Kevin Federline, is smoking and watching a black-and-white video of Spears on a projection screen.
She then entered a dressing room with mirrors, wearing lingerie, high heels, stockings and a short fur jacket. She proceeds to a bedroom, in which a black dress is laid out on the comforter. She puts on the new dress and the camera cuts to the party outside where people gathered waiting.
During the song's bridge, it is revealed that the party is actually Spears's wedding, as she starts walking towards the aisle and Federline waits next to a priest. The video ends with a shot of the black-and-white video and Spears looking into the camera.
The black-and-white footage was released as an alternate version of the music video in the 2004 DVD Greatest Hits: My Prerogative.