The main character of the story is a young and promising guy named Saionji. He gets a job at a research company, where Reiko becomes his immediate supervisor. Reiko instructs Saionji to test the company's revolutionary product, a powerful pheromone—based drug that is an aphrodisiac for all the girls working at the company.

Hentai was created based on a visual novel titled "Kunoichi Sakuya Shinobishi Omoi wa Chijoku ni Nurete..." from Rune Studio. Kunoichi are female ninja who undergo special training to perform dangerous tasks and assassinations. The kunoichi training program includes various tests that test their willpower, endurance, speed, and stealth attack skills.

Ryusuke decides to kill the head of the Kamair bandits, but everything went awry. The guy would have been captured if not for his sister Misa, who sacrifices herself and changes him for herself. Ryusuke is looking for companions to save his sister, and a girl named Makoto comes across who has scores to settle with the robbers.