Detective Opera Milky Holmes

During an encounter with a group of Gentlemen Thieves, the ace detective group Milky Holmes suddenly lose their Toys, which give them special abilities. A month later, they have since descended to being the worst student at Sherlock Holmes' Detective Academy. The Gentlemen Thief leader, Arsene, masquerading as the Student Council President, moves Milky Holmes into a less luxurious lifestyle inside an attic and gives them three months to recover their toys before they are expelled.

As the Gentlemen Thieves continue their crime spree, Milky Holmes are having trouble adjusting to the poorer life. Cordelia Glauca tries to convince everyone to be friends, but inadvertently makes things worse. Everyone's mood soon livens up when Sherlock Shellingford finds a stray kitten, naming it Kamaboko. When Kamaboko starts pilfering bread from the cafeteria, Milky Holmes are accused of stealing it. Wanting to protect the kitten, Cordelia takes the blame. In order to save Cordelia from expulsion, Milky Holmes investigate the crime scene, finding the true culprit and the reason Cordelia protected him. Learning the truth, Henriette revokes the expulsion and allows them to keep the cat.

When Milky Holmes go to assist the guarding of a statue targeted by the Gentlemen Thieves, they are teased by the anti-Gentlemen-Thief force, G4, with false promises of getting their toys back. When Hercule "Elly" Barton fails the ridiculous ritual set by the G4 leader, Kokoro Akechi, Nero Yuzurizaki gets angry at her. When Arséne steals a fake statue, G4 try to follow them with a tracking device, but Milky Holmes accidentally breaks their computer when Cordelia gets scared. Still sad about earlier, Elly runs off so the others go look for her at the museum, where they run into the thieves who are trying to find the real statue. During the fight, Cordelia and Twenty get trapped in a sarcophagus, but the embarrassing noises temporarily gives Elly her toy back allowing her to get them out.

Milky Holmes and G4 are informed about a girl named Irene Doala who went missing in the Yokohama woods. While searching for her, Sherlock and Kokoro become separated from their respective groups, winding up in a cave along with Irene. Irene explains she got lost while finding a treasure chest so she can stop her father's company from going bankrupt. When a bear attacks them on their journey back, Sherlock makes several failed attempts to rescue them only be coincidentally saved by an unexploded bomb. They are later found by G4 and returned home.

While trying to rescue Kamaboko from traffic, Elly is saved by two girls named Mary and Kate. They are revealed to be thieves, who attempt to kidnap Kamaboko, but are halted when Milky Holmes spot them and, mistaking them for detectives, invite them in. However, they soon manage to escape with Kamaboko, plotting to torture him due to his resemblance to their old boyfriend. As Milky Holmes search for him, Stoneriver, Twenty and Rat find Mary and Kate and fight against them for disturbing their territory, but are overpowered by their toys. Mary and Kate nearly take Kamaboko again, but change their mind when he saves them from one of Rat's bombs.

The Princess of Marlo, Claris, who bears a striking resemblance to Sherlock, doesn't want to get married to a prince in order to support their country. Wanting to be a normal girl, she runs off and finds Sherlock and offers to trade lives with her for a day. While Claris hangs out with the rest of Milky Holmes, Sherlock spends the day with her prince-to-be, Pero, who is a masochist with a catgirl maid fetish. As Claris contemplates staying in this new life, her identity is discovered by Henriette, who tells her to stop running away from her troubles. Getting the help of Milky Holmes, Claris gets to the church before Sherlock gets wed to Pero, revealing she will reach her dreams with her own hands. Pero reveals he had been trying to get her to put off the marriage, as he was in love with her grandmother, who he marries, connecting the two countries after all.