"Green Green" is a 12-episode anime series set in the fictional Kanenone Gakuen, an all-birls boarding school located in a remote mountainous area. The school undergoes a temporary merger with an all-boys school, leading to the arrival of male students on campus. This sudden integration creates a mix of excitement, chaos, and romantic tension among the students. The story primarily centers on the interactions between the male and female students, exploring themes of adolescence, relationships, and self-discovery.

The protagonist, Yuusuke Takasaki, is a shy and reserved boy who becomes the focal point of attention due to his kind nature and unintentional involvement in various comedic and dramatic situations. His arrival at the school coincides with the introduction of other male characters, including the energetic and mischievous Ichibanboshi Tenjin and the stoic and mysterious Bando Takahiro. The female students, such as the cheerful and outgoing Midori Chitose, the quiet and introspective Futaba Aoi, and the strict yet caring class representative Megumi Tanaka, each bring their own personalities and dynamics to the story.

The narrative unfolds through a series of episodic events, blending comedy, romance, and occasional moments of drama. The male students struggle to adapt to their new environment, often finding themselves in humorous or awkward situations as they navigate their relationships with the female students. Romantic subplots emerge, particularly between Yuusuke and Midori, whose interactions range from lighthearted banter to moments of genuine emotional connection. The series also explores the challenges of communication and understanding between the genders, as well as the personal growth of the characters as they confront their insecurities and aspirations.

A recurring element in the story is the presence of a mysterious girl named Wakaba, who appears to have a connection to the school's past. Her enigmatic nature and cryptic behavior add an element of intrigue to the otherwise lighthearted narrative. As the series progresses, the characters uncover more about Wakaba's identity and her ties to the school, culminating in a resolution that ties together the various plot threads.

"Green Green" balances its comedic and romantic elements with occasional moments of introspection, offering a portrayal of teenage life and the complexities of relationships. The series concludes with a sense of closure, as the characters reflect on their experiences and the bonds they have formed during their time at Kanenone Gakuen.