Mitsuhiko tells the Detective Boys that Shouko Amemiya, a girl that strongly resembles Haibara, is missing. Conan considers the possibility that the Black Organization kidnapped her and investigates.

From Amemiya's strange behavior the Detective Boys head to a garage where they find kittens Amemiya had been tending. Unable to find Amemiya, they investigate the area around the garage and realize there had been a recent car accident.

A client named Atsushi Misumi asks Kogoro to search for his girlfriend, Ami. Deducing from her last words, they realize Ami is waiting for Misumi at the place where they first met. They are driven by Misumi to Gunma Prefecture where they find Ami in a sealed up car dead.

After investigating, Conan realizes how the murder was done.

Mōri, Ran, and Conan are at a café when they run into Takagi who is aiming to pick up girls. Meanwhile, he finds Sato there doing the same. After a tense date with two strangers, Conan realizes from the conversation that a boy home alone is in danger. When they arrive at their house, the boy has been kidnapped. The kidnapper leaves an email demanding money.

After solving clues Takagi leaves suddenly and Conan reveals who the kidnapper is.

Kogoro and Conan visits a famous author named Osamu Umezu in order to have his book signed. Later they spot Osamu's secretary, Mikami Touru, running to Osamu's house. They learn that Mikami that Osamu is not answering his phone calls and he was going to check up on him. They accompany him to Osamu's apartment and find Osamu dead. Evidence suggests it was suicide but Kogoro notices blood on the trash bin and reveals that it was a murder.

Conan and Ran pass by a dog park and befriend two couples whom each own a dogs; one is named Musashi and the other is named Coeur. Yoriko Nakatani, the neighbor of the owner of Musashi, the Tsutsumi couple, asks Kogoro to investigate the dog Musashi who acts aggressively to her. Conan and Ran disclose they believe she did something to upset the dog, causing her to leave. The next day, Nakatani's mother in law is seemingly killed by Musashi when his teeth marks are found on her throat.

A free-lance writer comes to do a story about the Detective Boys. They go along with their teacher to the writer's apartment, but when they arrive they find that he has been bludgeoned to death.

Three out of the four messages on the answering machine are suspect, but in each one there is something going on which helps them verify the time and place of the call

Aya, who made a promise with Shinichi, comes back to his house to ask help for a case involving her grandma and her daughter that died at the age of 17.

The waitress of Poirot Cafe, Azusa Enomoto, reported she received strange messages from a boy, suggesting he might be kidnapped or trapped in a location without food and water. The only way to find him is by reading his text messages. The boy only knows how to send, but does not know how receive. Conan must put the clues he gives together to find out his location.

A man named Sasamoto is nearly killed by a falling cinder block. He believes that it's his old college friend, Hikage, who disappeared 3 years ago, but since has written a murder prophesy novel where he kills his 3 friends from college

The Detective Boys visit a Kamen Yaiba Stunt Show. The director, Shinji Fukamachi, and assistant director, Hidehiko Nakasato, scold the stunt driver, Kengo Rikiishi, for doing such a dangerous stunt with the car. Later, Kengo dies on impact and the Detective Boys investigate

Kogoro and Conan are brought to an apartment to examine the death of a man named Yamamoto. It is presumed a suicide as evidence project he put a gun in his mouth and firing.

A struggling artist named Daijirou Manaka is nearly killed by a falling I beam. While he's lying in the hospital Takagi and the Detective Boys go through his bag and find his license, a rope, a pair of gloves, and a suicide note. Daijirou wakes up and when Takagi asks him about the bag he claims to have amnesia, but Conan notices he is lying.

The Junior Detective Club are at the beach digging up clams. Soon they encounter a college group of students on similar excursion. Later, however, one of the college boy is found dead from poisoning in the car in which they had ridden

Conan is convinced that this is murder and, with the help of Detective Boys, recovers evidence to confirm his theory and the offender is arrested.

Kogoro is asked by a man to solve a coded text message from his daughter since she refused to tell him the meaning of the text message.

Sonoko, Ran, Eisuke and Conan were hiking to Sonoko's mountain villa when they discovered the bridge leading to the lodge had collapsed due to disrepair. Out of range of mobile phone signals, they went to a neighbouring villa to request the use of the house phone. They learned that it was recently bought over by a music group "Dorcus" as a den for composing new music. The band members revealed that they got the villa dirt cheap as it was supposed to be haunted.

Inspector Misao Yamamura arrived to investigate. Conan also tries to gather clues to help, but is limited to what he can do when a sneaky Eisuke starts to spy and watch him. Conan has to use different tactics so he won't seem suspicious to him.

They make a stop by a famous Rakugo actor's restaurant, Meguro. The Rakugo actor, Ichimatsu, helps out at this shop with Meguro Miya, ex-wife who is also the owner. After the play, Ichimatsu is stabbed and sent to the hospital.

Takagi and Miyamoto poses as a bride and groom in order to catch a serial killer/burglar who had threatened to kill the real bride and groom.

A famous magician hires Kogoro to keep watch on his staff members, as he believes one of them may be out to kill him.

Conan fishes around for clues in hopes of finding the true culprit. By the short trip close to the stage, Conan got some clues to resolve the case. After gaining info, he learns who's behind the trick, and exposes the true mastermind behind the death of the magician.

Conan, Ran, Mouri, and Sonoko travel to Shikoku to see the kabuki play Phantom of the Konpira. It is a play based on Phantom of the Opera. Things start to mimic the play.

A man buys a ticket to see a movie, which is a sequel to another he and his friends have seen in the past. He gives his ticket to one of his friends, then leaves, but clues he has left behind leads Conan to believe that he has more on his mind.

Manda, a well-known author, is greeted by his editor who needs his manuscript. He tells him that he is almost done and the editor goes and waits in the hotel hallway. Manda sneaks by in a disguise and goes to Haramoto's house, a man who has been ghost writing for Manda. Haramoto gives Manda the script and then tells him about a new mystery he is planning to unveil once Manda introduces him to the right people. Manda kills Haramoto with a vase and steals the detective story before returning to his hotel room.

Genta hits a baseball through the window of Haramoto's house and breaks a vase. They go inside to apologize and find Haramoto dead. Conan realizes that the victim must have known the killer, and Manda is acting suspicious especially when he interrupts the housekeeper when she mentions the mystery Haramoto was working on.

A murder occurs in an apartment. The victim is a famous detective author. A card left in the scene shows that the somebody who called himself as character of the author's detective novel took the life of the author. Two suspects were identified: the guard of mansion who likes to drink despite author telling him not to, and the editor of the publishing company who claimed that the author was alive when he left the room. After finding evidence through sushi, the culprit was revealed to have done it out of love for the author's mystery

Sonoko brought Ran, who in turn brought Conan, to visit the site in the countryside used as location in the filming of a well-received romantic TV series, where the lead actress tied a red handkerchief to a tree branch to enable her lover to find her.

The murder investigation narrowed to three suspects who were recent arrivals at the nearby inn. Conan deduced the culprit and the cause of the murder.

The Junior Detective Club visited An overly strict man, since Ayumi and Mitch suggested to interview him. Later, however, the Club Crews just have seen that the overly strict man is accused of murdering a woman. Is it murder or is it self-defense? Conan must investigate and figure out the truth.

The teacher of the Detective Boys decides to give the class a mental test. Conan is called by the teacher so the class must solve it without him.

A rockstar named Roku Itakagi has been missing for the past few days. A young boy named Takumi Hashiratani claims that on New Year's Day, he witnessed a man carrying Itakagi in a bag and throwing him over a bridge.

While investigating, they learn that Itakagi's band logo was of a snake with nails piercing through it. After questioning a tattooist, they learn that the tattoo was new and only three people have gotten it.

Eisuke asks Kogoro to investigate a mystery and believes it is crime related to The Red-Headed League

After a thorough investigation, Conan tranquilizes Kogoro and reveals the culprit.