Green Green takes place in the countryside of Japan, at the isolated all-male boarding school of Kanenone Gakuen (translated literally in English as "Sound of the Bell Academy"). Since there are no females for miles, the school is advertised as the "last remaining paradise for men on Earth". The Kanenone school board has begun talks to merge with an all-girl boarding school, in hopes of becoming a co-ed boarding school. This has the hormone-driven, girl-deprived male body of Kanenone thrilled.

Both schools decide to have a test run of sorts, having the girls from the all-girls school stay at Kanenone for a few weeks, in order to see how the boys and girls get along. Yuusuke Takazaki, the main character, has his hands full with his "perverted" roommates, nicknamed the Baka ("Idiot") Trio. The Baka Trio - which consists of Bacchi-Gū, a fat pervert, Ichiban-Boshi, a self-proclaimed ladies man, and Tenjin, a gentle giant who has a "little sister" fetish - are incredibly excited that there will be girls around.

Futaba Kutsuki (朽木 双葉 ,Kutsuki Futaba?)

Futaba plays the role of the tough, boy-hating tsundere. She is less than enthusiastic about the co-ed trial run of the schools, and acts as the self-appointed protector of the girls against the boys of Kanenone. She is particularly disgusted by the antics of the Baka Trio, and does not hesitate to resort to physical violence against them as punishment for their indiscretions. After the Baka Trio pulls a humiliating prank on her, she decides to leave Kanenone immediately on her own. She gets lost and injured in the surrounding woods but is rescued by Yuusuke, who carries her back to Kanenone. This act of kindness, along with an earlier display of chivalry by Yuusuke to protect her modesty, sparks feelings inside her for the boy, and Futaba soon finds herself falling in love with Yuusuke. The two become a couple in Episode 13.

Futaba has a younger sister, Wakaba. She is also the main character in the H-game's second sequel, Green Green 3.

When the buses containing the girls arrive, one girl named Midori Chitose excitedly disembarks first, leaping at and happily hugging a confused Yuusuke. Who is Midori and how does she know Yuusuke? The series focuses on answering this question and the antics of the Baka Trio.