Freshman Kaho Nikaidou is from an influential family, and as such, no one has ever said anything even remotely mean to her, for fear of incurring her household's wrath. Wishing to be around people who will not treat her as special because of her background, she leaves home to live at a dormitory for her new school year. Shortly after arriving, Kaho accidentally wanders into traffic and is saved by a tall, handsome stranger. When she asks for his name, he tells her she is weird and walks away. Having finally met the only person to ever say an unkind word to her, Kaho falls head over heels for her savior. After meeting her rescuer yet again and discovering that his name is Kanade Takahashi, she confesses her love to him. Kanade says he would like for them to be a couple, but that Kaho may not want to date him after she finds out his secret. To her shock, Kaho discovers the startling truth: Kanade is a fifth grader! Deciding that she can't date a fifth grader, Kaho intends to break up with him. But as she spends more time with Kanade, she begins to care for him even more and continues dating him. Hatsukoi Monster follows Kaho's first steps into love with Kanade, her immature, yet kind, fifth grade boyfriend.

On the surface, Koudo Ikusei Senior High School is a utopia. The students enjoy an unparalleled amount of freedom, and it is ranked highly in Japan. However, the reality is less than ideal. Four classes, A through D, are ranked in order of merit, and only the top classes receive favorable treatment. Kiyotaka Ayanokouji is a student of Class D, where the school dumps its worst. There he meets the unsociable Suzune Horikita, who believes she was placed in Class D by mistake and desires to climb all the way to Class A, and the seemingly amicable class idol Kikyou Kushida, whose aim is to make as many friends as possible. While class membership is permanent, class rankings are not; students in lower ranked classes can rise in rankings if they score better than those in the top ones. Additionally, in Class D, there are no bars on what methods can be used to get ahead. In this cutthroat school, can they prevail against the odds and reach the top?

Amaumi Haruhiko is a high school student who attends Shimano Academy in a town called Narasakicho. Narasakicho contains an unknown rainbow which constantly overlooks the town and is related to granting a magical wish called "Gift." Gift is a once-in-a-lifetime present between two people. As a child, Haruhiko has been close with his childhood friend, Kirino, until he obtains a new non-blood sister by the name of Riko. Haruhiko develops a strong relationship with Riko until they sadly depart due to the fact Haruhiko's father could no longer support the two of them. After some times passes by, Riko finally returns to the town of Narasakicho, and along with Kirino, starts to attend Shimano Academy with Haruhiko. The series revolves around the relationship among these main protagonists and slowly reveals the story behind both Gift and the rainbow.