"Gekijōban Tantei Opera Milky Holmes: Gyakushū no Milky Holmes" is a film adaptation of the "Tantei Opera Milky Holmes" anime series, which revolves around a group of young detectives with supernatural abilities known as "Toys." The story is set in a fictional world where detectives and thieves possess these unique powers, and the balance between them is maintained through their ongoing conflicts.

The film centers on the Milky Holmes detective team, consisting of four girls: Sherlock Shellingford, Nero Yuzurizaki, Elly Cunningham, and Cordelia Glauca. Once renowned for their detective skills and Toys, the group has fallen into obscurity after losing their powers. However, they remain determined to regain their former glory and continue solving mysteries. The narrative begins with the team investigating a series of strange incidents involving a mysterious figure known as the "Phantom Thief Empire," which threatens the peace of their city. As the Milky Holmes team delves deeper, they uncover a plot that challenges their resolve and forces them to confront their own limitations.

The plot thickens as the team encounters familiar adversaries, including Arsène and her gang, who are also entangled in the unfolding events. The story explores themes of perseverance, friendship, and self-discovery as the Milky Holmes team works to overcome their weaknesses and reclaim their status as elite detectives. The film incorporates elements of comedy, action, and mystery, staying true to the tone of the original series while expanding on its lore and character dynamics. The climax involves a high-stakes confrontation that tests the team's unity and determination, ultimately leading to a resolution that reaffirms their bond and commitment to justice.