The movie starts with a comic-book style cartoon explaining that in the future people's organs will stop working; leading to one company having all the viable organs for transplants. That company is GeneCo, and it is run by Rotissimo Largo (played by Paul Sorvino) and his three children. Each of them having , one likes to stab people, another is always having surgery, and the third will sleep with anything with a pulse. Geneco is so powerful that they had a law allowing repossession of peoples organs if they default on payments.
With that exposition out of the way the story mainly focuses on Shilo, a young girl whose mother died when she was born and is suffering from a sickness that forces her father Nathan (played by Anthony Head ) to be very protective and sheltering of her. It turns out Largo wants Shilo to be his replacement as the head of GeneCo after his demise, because he feels that his children are not good enough to carry on the Largo name, but it also turns out he is blackmailing Nathan so that Nathan will be a Repoman. Largo even goes as far as to use the fact that Shilo's mother died during childbirth as blackmail so that Nathan will do what he wants, despite the fact it was Largo himself that poisoned her. There is also Blind Mag a famous opera star who has had an eye transplant due to her working as Largo's personal singer. she no longer wants to work for Largo but if she quits her eyes get repo'ed.
All these subplots come together in the final act which takes place at the Genetic Opera, a night of opera sponsored by Geneco. Blind Mag dies rather than work for Largo. Nathan and Shilo reconcile, just in time for Nathan to be shot by Largo, who in turn also dies. Leaving Shilo the head of Geneco even though she didn't want the power.