"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, haunted by guilt over Menma's death. One summer day, Menma's ghost appears before him, claiming she cannot pass on to the afterlife until her unfulfilled wish is granted. Unsure of what her wish is, Jintan reluctantly reunites with his estranged friends—Naruko "Anaru" Anjo, Atsumu "Yukiatsu" Matsuyuki, Chiriko "Tsuruko" Tsurumi, and Tetsudo "Poppo" Hisakawa—to help Menma move on.

As the group reconnects, old tensions and unresolved emotions resurface. Yukiatsu harbors deep resentment and jealousy toward Jintan, while Anaru struggles with unrequited feelings for him. Tsuruko, who has always been in love with Yukiatsu, feels overshadowed by his lingering attachment to Menma. Poppo, the most carefree of the group, tries to mediate their conflicts while grappling with his own guilt over the past. Together, they confront their shared grief and the ways Menma's death fractured their friendships.

Throughout the series, Menma's presence forces the group to confront their memories of her and the unresolved issues they carry. Flashbacks reveal the close bond they once shared as children, contrasting sharply with their fractured relationships in the present. As they piece together clues about Menma's wish, they gradually come to terms with their guilt, regrets, and the impact of her death on their lives.

The narrative builds toward an emotional climax as the friends finally understand Menma's true wish: to bring them back together and help them heal. In the final moments, Menma's spirit is able to move on, leaving the group with a renewed sense of closure and the strength to rebuild their friendships. The series concludes with a poignant farewell, emphasizing themes of loss, reconciliation, and the enduring power of childhood bonds.