Green Green is set at Kanenone Gakuen, an all-male boarding school in the Japanese countryside, where life has become painfully dull because there are no female students for miles around. To address the social and psychological strain, the school board arranges a bold experiment: Kanenone will merge with the nearest all-girl boarding school and become co-ed. The boys are thrilled at the prospect, while the girls are curious about what school life might be like with boys nearby. Before any final decision is made, the girls are invited to stay at Kanenone for one month as a trial.
At the center of the chaos are Yuusuke Takazaki and his mischievous roommates, the Baka (Idiot) Trio, who must somehow navigate life around the incoming students without making complete fools of themselves. When the girls arrive by school bus, the atmosphere turns immediately weird, hormonal, and hysterical. One girl in particular, Midori Chitose, leaps off the bus and immediately embraces a very confused Yuusuke, leaving everyone to wonder whether he is a natural ladies' man or whether the two of them share a history that he is not yet aware of.