Akane is a very chaste, very conservative nun who is the caretaker of Sabu, an elderly gentleman who is basically comatose. They live alone in a house on the beach, abandoned by Sabu's family who refused to care for him anymore. One day, Akane finds that there is an intruder in the house, Kayoko, who had escaped a depraved sexual encounter nearby with a couple of guys. As if things weren't crazy enough, another two random people show up at the door. Rine is a teacher that has run off with a student of hers, Shinji, and they are looking for a place to hide (and to do bad things to each other).
Naked Desire follows these people as they try to survive together away from society, not knowing that detectives are in hot pursuit after Shinji is determined missing by his family. Akane must decide whether to stay true to her faith and remain pure, or give in to her ultimate desires like Kayoko, Rine and Shinji.