"Tantei Opera Milky Holmes" is set in a fictional world where individuals possess special abilities known as "Toys," which grant them unique powers. The story centers on four young girls—Sherlock Shellingford, Nero Yuzurizaki, Elly Himeyuri, and Cordelia Glauca—who form the detective group Milky Holmes. They attend Holmes Detective Academy, an institution dedicated to training aspiring detectives. Each member of the group possesses a Toy: Sherlock has telekinesis, Nero can manipulate objects, Elly can read minds, and Cordelia can control magnetism. Together, they solve mysteries and aim to become great detectives.

The narrative begins with Milky Holmes as a celebrated detective team, admired for their skills and success. However, their lives take a turn when they lose their Toys during a confrontation with the Phantom Thief Empire, a group of thieves who also wield powerful Toys. Stripped of their abilities, the girls are demoted to the lowest rank at the academy and must navigate their new reality while striving to regain their lost powers. Despite their setbacks, they continue to take on cases, often relying on their wits and teamwork rather than their former supernatural abilities.

The Phantom Thief Empire, led by Arsène and her accomplices, serves as the primary antagonistic force. Arsène is a cunning and enigmatic figure who frequently clashes with Milky Holmes, challenging them with elaborate heists and puzzles. The dynamic between the two groups is a mix of rivalry and occasional reluctant cooperation, adding complexity to their interactions.

Throughout the series, the focus shifts between comedic and lighthearted moments, often highlighting the quirky and exaggerated personalities of the characters, and more serious detective work. The girls’ determination to improve and their unwavering friendship form the emotional core of the story. Supporting characters, such as their strict instructor Henriette and the bumbling Inspector Lestrade, contribute to the series’ humor and world-building.

The anime blends elements of mystery, comedy, and slice-of-life, creating a balance between episodic cases and overarching plotlines. The loss and eventual recovery of the girls’ Toys serve as a central narrative thread, driving their growth as detectives and individuals. The series also explores themes of perseverance, teamwork, and self-discovery, all while maintaining a playful and whimsical tone.