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.

The Detective Boys are doing a book report when Ayumi notices that the last page to her book, Alec's Adventure, has been torn off. Conan and Ayumi decide to search for Tsukasa Naito, the one who burrowed out the book last.

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.

The Detective Boys are at a small ski resort and meet up with four graduate students who are building a snowman for an art project. Later that evening, Sakuko Kokura, one of the graduate students, become lost in the blizzard and the two groups begin their search for her. Conan finds the Kokura dead at the bottom of a cliff in a lake. The police declares that Kokura's death was a snowboarding accident. Conan notices that the body is missing a hat, goggles, and gloves and believes that she was murdered and one of the graduate students is the culprit.

Conan realizes how the murder was done and gathers the suspects along with inspector Misao Yamamura.

The Junior Detective League head to a pond to witness animal control officers attempting to capture an alligator snapping turtle that is loose in the wild.

Takeyori Oikawa claims that the Phantom Thief Kid is targeting his painting which is to be unveiled to the world live that day. The painting is a final part of a set of four. He hires Kogoro Mori to protect the painting from Kid.

After a thorough investigation, Conan concludes there was never a painting behind the cloth and that it was suspended by a fishing line.

Kogoro takes Ran Mori and Conan to an onsen in a rental car after being given a special deal. Kogoro then receives a call from Inspector Megure who reveals that a bomber called the police station to tell them a bomb was placed on Kogoro 's car and will detonate when his speed goes below twenty km/h.

Conan's class finds a wallet with a message from Ran ten years ago. Conan shares the story of how it got there by explaining the adventure he had in the past.

Shinichi solves the riddle and heads to the school and finds the next riddle on a stop sign. Back in the present time, Conan realizes what the riddle actually means.

Eri Kisaki is visited by Ran and Conan who came to remind her it is the anniversary of her first date with Kogoro

Kogoro takes Conan out to look for a restaurant in the city and witnesses a hit and run resulting in two pedestrians being injured. A witness reveals he saw the car waited for those two before speeding into their direction and Conan concludes it was an attempted murder.

Agasa takes the Junior Detective League to a cheesecake bakery. Genta however decides to remain in the underground parking lot and continues to kick a soccer ball against a wall. When Genta hears a strange sound, he misses his kick and subsequently losses balance and falls on his head causing him to lose consciousness

The police gather the three suspects together where Conan reveals the culprit

Kogoro, Ran, and Conan are in a mall when a murder occurs on the third floor. The police arrive and seal the mall preventing people from leaving the third floor and preventing public access to the mall.

Kogoro, Ran, Conan, Heiji Hattori, and Kazuha Toyama are at a festival when a monk asks them to solve a case of a disappearing body at the temple.

A hostess named Hiroko Inoue is found dead in her home by Osamu Kitzuka, a colleague of Inoue's to be husband Akira Taokaoka. Kitzuka had a planned meeting with Taokaoka on that day and was the reason he found the body. As Kogoro and Conan investigate, the police conclude it to be a random burglary after Taokaoka's alibi proves he was at Fukushima Prefecture during the time of Inoue's death.

Agasa takes the Junior Detective League camping, they end up being stranded in the middle of the woods. They decide to ask for lodgings from a house owned by an elderly woman named Iwae Tanaka. At the same time, Akane Ooba and her two hosts, Raito Adachi and Fuuga Kahara, also request for lodging and Tanaka complies. That night, Mitch goes to the restroom but sees something horrifying causing him to run back to his room

Tanaka dismisses Mitsuhiko's accusation as his imagination and the police continue their investigation. As Conan investigates he realizes who the murderer is.

Conan and the Junior Detective League run into Amy's neighbor, Yasuyo Akimoto, who is searching for a kind bearded policemen who she ran into multiple times last week. At the police station, they reveal they do not have an officer like that and it was against police regulation to have facial hair.

Hattori tells Conan he found someone that has knowledge on Ethan Hondou's father; However that person is dead but his grandson, Souhei Nishigun, has a photograph of Ethan's father. Conan, Vi , and Agasa travel to Nishigun's apartment and realize that someone has stolen Nishigun's photograph album and deleted the data off his computer.

Nishigun phones all three of his friends to ask what they were doing during the time of the robbery. Conan realizes who the culprit is from the phone calls and reveals the culprit.

Conan and Vi rescue a kitten from a tree and return him to his owner, Tamotsu Ishigami, the owner of a local café. A woman barges into the café exclaiming she found her boss, Kenzo Kanemaru, dead.

Kogoro is invited to attend an interview of the mystery book writer Masataka Moroguichi. The next day, Moroguichi is found dead from consumption of poison. The room was locked and the key was in Moroguichi's palm; The only opening to the room is a small window which can only fit a small child.

Yoko Okino takes the Junior Detective League to a TV studio for a tour. When they run into Onizuka Satan, a vocalist for a visual kei rock band. The Junior Detective League decide to search for his room to get his autograph.

Eri Kisaki is asked to defend Hiroaki Takeuchi who had been accused of Hit and Run incident. However the evidence suggests it was his wife, Mariko Takeuchi, who was committed the crime.

Hattori tells Conan that he met a better Detective than Conan during his middle school years and reminisces about the case.

Conan, Ran, and Sonoko are visiting a sick friend in the hospital. There they meet Eisuke who tells them he is searching for his long lost sister who looks identical to Rena Mizunashi.

Conan suspects there is a hidden component to Eisuke's story and believes Eisuke is searching for Rena with an ulterior motive.

Kakuzō shows Kogoro a photograph of Tango's body in a pool and points to a white glove Tango is wearing. He reveals that the glove was the same glove their previous butler wore before a car accident killed him, and that Tango's murder occurred on the anniversary of the butler's death.

Conan's investigation leads him to realize how Kakuzō and Tango's murder was accomplished.