Hikari Tsutsui finds life much simpler within the confines of his two-dimensional reality. Awkward and lacking social skills, he finds solace in video games and anime. Sadly, his classmates ridicule and ostracize him for his odd behavior, leaving Yuuto Itou as his only friend. Yuuto is equally enthusiastic about gaming, but he likes to wear cat ears. While being punished for tardiness with pool cleaning duty, Tsutsui meets Iroha Igarashi. However, he tries to avoid her because of her infamous reputation. She is blunt, disliked by girls, and notorious for messing around with boys, and Tsutsui believes any association with her would lead to trouble. The story in 3D Kanojo: Real Girl revolves around two outsiders: one, a boy ruled by emotions he has yet to fully encounter, and the other, a girl attempting to break him free from his shell.