"Anohana: The Flower We Saw That Day" centers on a group of childhood friends who drift apart after the tragic death of one of their members, Meiko "Menma" Honma. Years later, the protagonist, Jinta "Jintan" Yadomi, lives as a reclusive high school dropout, disconnected from his former friends. One summer day, Menma's ghost appears to Jintan, claiming she cannot pass on to the afterlife until her wish is fulfilled. However, Menma cannot remember what her wish is, prompting Jintan to reunite the group to help her.

The story explores the emotional scars and unresolved guilt each character carries from Menma's death. Naruko "Anaru" Anjo, a classmate harboring unrequited feelings for Jintan, struggles with self-esteem and her perception of others. Atsumu "Yukiatsu" Matsuyuki, outwardly successful but deeply conflicted, harbors feelings for Menma and resents Jintan. Chiriko "Tsuruko" Tsurumi, Yukiatsu's childhood friend, hides her own feelings for him while maintaining a composed exterior. Tetsudo "Poppo" Hisakawa, the most carefree of the group, uses humor and travel to mask his pain.

As the friends reluctantly come together, tensions rise, and long-buried emotions surface. The group grapples with their shared past, their individual struggles, and the reality of Menma's presence, which only Jintan can see at first. Through their interactions, they begin to confront their guilt, regrets, and the impact of Menma's death on their lives. The narrative builds toward a poignant resolution as they work to uncover Menma's wish, ultimately leading to a heartfelt farewell that allows both Menma and the group to find closure.

The series balances themes of grief, friendship, and healing, portraying the complexities of human emotions and the enduring bonds of childhood connections. The characters' growth and the resolution of their shared trauma form the emotional core of the story, making it a deeply moving exploration of loss and reconciliation.