Kanenone Gakuen is an all-male boarding school situated in the Japanese countryside. While an all-male institution is not unusual, life can grow quite difficult when there are no female students for miles around. To support the psychological well-being of everyone involved, the school board has decided to attempt a merger with the nearest all-girl boarding school to become co-ed. The boys of Kanenone are more than thrilled by the prospect, and the girls are curious about how interesting school life might become with more boys around. Before any serious decisions are made, the girls have been invited to stay at Kanenone for one month as a trial. Green Green follows Yuusuke Takazaki and his mischievous roommates, known as the Baka (Idiot) Trio, and their ability to converse with the girls without making complete fools of themselves. However, as soon as the school bus carrying the girls arrives, things become weird, hormonal, and hysterical. In particular, a girl named Midori Chitose leaps off the bus and immediately embraces a very confused Yuusuke. Is he a natural ladies' man, or do the two of them share a history that he is unaware of?