Conan, Kogoro, and Ran all attend a concert at a local department store. After the drummer, Yuusuke Nakamura, hears about a CD Ran is searching for, he tells her to follow him to the storage room where he has a copy of it. While there, they discover the lead vocalist, Yukiko WaTanbe, dead in the storage room.

Conan, Kogoro, and Ran pass through Mount Fuyana on their way home and are stopped by Misao Yamamura who instilled a road block in order to catch the Silver Witch, a woman who drives a White FD car and challenges people in a drag race.

Later that day, Conan realizes the culprits created a mirage of driving into the air and tells Kogoro they shall capture the witch tomorrow. The next day Conan reveals the pair with the fishing gear to be the culprit.

A man named Ryousuke Oomine threatens Kazuyoshi Onda, the president of a game company, to pay his game designer the money he deserves. During the dispute, Oomine accidentally shoots Onda with a gun and leaves the crime scene. The next day, Ran and Sonoko take Conan out to an ice-cream parlor in the mall. Conan overhears Takagi and a police officer discuss the how a young girl has been kidnapped and held hostage by Oomine. Conan searches for the girl at the parking lot and frees her from Oomine's grasp. However, Oomine captures Conan and uses him as his hostage.

At Agasa's house, Oomine reveals the gun he bought was supposedly filled with blanks and it was only used to scare Onda. After Onda was shot, he reveals he threw the gun away. Conan, Oomine, Ran, and Kogoro decide to search for the gun.

Agasa takes the Detective Boys to a revolving sushi shop. While there, Ryuuzou Agatsuma, a food critic, collapses by cyanide poisoning.

While investigating, Conan realizes Ryuuzou was left-handed and finds out how the murder was done. Using his voice changing bowtie, Conan impersonates Agasa and reveals the culprit

Genta's father is in a competition where anyone with the surname Kojima are allowed to participate. Conan and the Detective Boys attend to watch the competition after hearing Genta's father making past the preliminary rounds as one of the three finalists. When it is announced the competition is canceled, Conan notices the announcer has blood on his sleeve and investigates

The police interrogate the three finalists and learn all three culprits share the same shoe size, voice, and were all left handed

Two men named Fumitaka Togashi and Tsuneo Hakamada are released on parole. The next day Togashi is convicted for the murder of parole officer Takehiko Sakuraba. Kogoro attempts to persuade Togashi who has taken an oath of silence to tell him everything about the murder.

Kogoro and Ran take the Detective Boys to an onsen in Kinosaki, Hyōgo so Conan can heal his sprained ankle. While there, Ran runs into a little girl named Haruna. Ran learns that Haruna is by herself and accompanies her around Kinosaki and remains unaware that a mysterious man is secretly stalking the pair.

Haruna is found unconscious and taken to the hospital. While her parents are arguing, Haruna sneaks out of the hospital after remembering that the man threatened to kill Ran if she did not deliver the "Rainbow Child" to him.

While driving home, Kogoro, Ran, and Conan witness a traffic collision between a green car and a red car. The man in the red car, Shun Hayami, dies from the collision due to his car catching fire. While the police interrogate Seiji Kurumatani, the man in the green car, he claims that he did not see the car at the intersection which caused the accident.

Agasa and Haibara become stranded when their car breaks down. They receive a ride from a suspicious man and woman. Haibara suspects they are part of the Black Organization when she learns that they are interested in meeting with Kogoro's assistant, Conan and how the man wants to show them his "half-kill".

Yamato and Euhara takes Kogoro, Ran, and Conan to a mansion. Euhara reveals that the mansion was owned by a rich man in the past. The man one day decided to search for five talented people and gave the five a room in the mansion until they have reached their dreams.

Yamato tells Koumei to take Ran and Conan with him to investigate the four suspects.

Koumei investigates the crime scene at the mansion and realizes who the culprit is. Before he could text his answer to Yamato, he is knocked unconscious by the culprit

Koumei regains consciousness, together they conclude that they lack the evidence to capture the culprit and thus decide to empty the Empty Fort Strategy to lure the culprit out.

Kogoro is hired by the Nijimura company to investigate a counterfeit company who has been copying their styles in handbags. Kogoro, Ran, and Conan witness the president of Nijimura become kidnapped by an unknown culprit.

Jodie Starling sees the deceased Shuichi Akai but dismisses it as an illusion. She heads to the bank to withdraw some money when a bank robbery occurs.

Conan manages to incapacitate one of the robbers and realizes the robber had changed into his clothes and realizes that the robbers plan to escape the bank by pretending to be the hostages.

Kogoro enters a barber shop and rests in a chair with a towel over his face. A few minutes later, a statue breaks and the owner, Ebihara, is found dead with a poisoned dart through his heart. Conan investigates and realizes who the murderer is.

Shigeko Ishikawa is being stalked by an unknown man. While Kogoro investigates, Conan is forced to watch over her two-year-old son nicknamed Santa. Ishikawa is later kidnapped by the unknown man and Conan investigates Santa's home in order to search for clues. Conan finds a feather of a White-eye and learns that Santa has been giving away figurines to people in the neighborhood. Conan realizes what the culprit's motive is after learning about the endangered counterpart of the White-eye, the Black-eye; He asks Santa to take him to the man who received the White-eye. Eventually ending at an abandoned pet store, Conan confronts the culprit and reveals that the culprit was intending to sell the endangered Black-eye to the underground economy and kidnapped Santa's mother when he perceived the White-eye figurine to be a threat. Conan clears the misunderstanding and explains Santa gave him the figurine as a friendly gesture.

Kogoro takes Ran and Conan to an onsen by the ocean. When they hear the sound of a boulder falling, they find a man named Hideaki Umezu, a mortgage company president, dead. The police presume that a boulder rolled off the hill and killed Umezu. However, Conan reveals that there are scratch marks around the spot where the bolder rested revealing that someone used the boulder to murder Umezu. The suspects are Umezu's secretary, his two daughters, and the onsen manager. After further investigation, Conan tranquilizes Kogoro and reveals the murderer to be onsen manager, Koichi Maekawa. Conan reveals that Umezu was not killed by the boulder but drowned, evidenced by the dirt under Umezu's fingernails revealing the struggle. Conan explains the boulder was used to create an alibi for Maekawa by using a wooden block connected to a line and buoy. When the tide lowered, the buoy pulled the wooden block and caused the boulder to roll off.

At the theaters, the Detective Boys run into Shiratori who is depressed since Sato's affection is being directed towards Takagi. Shiratori reveals that he is bind to Sato because of an encounter he had with her in the past. Shiratori explains Sato as a young girl stood up to two thieves by herself. Shiratori helps her stop the thieves and in return receives from her a drink with paper folded sakura. Conan questions if the girl was actually Sato as their personalities differ greatly. During the movie, Shiratori runs into a woman named Nami Kasakura who offers him a drink with paper folded sakuras causing Shiratori to consider the possibility she was the girl in the past. After the movie, Kasakura tells Shiratori she is being stalked and asks him to investigate. At her apartment, Kasakura's boyfriend is found dead. Conan suspects Kasakura but her alibi supposedly states she was at the theater the whole time.

Shiratori has Takagi search for the drinks at the theater and to bring them to the apartment. Shiratori reveals his deductions and explains that Kasakura drugged him with sleeping pills and placed her tuque on him to create her alibi by having Shiratori impersonate her. Takagi arrives at the department and shows them Shiratori's drink. Shiratori reveals that he had broken a piece from the flower design yet all the pieces remained on his drink revealing that Kasakura switched his drink while he was asleep to hide the fact there were sleeping pills in them. As further evidence, Shiratori explains that there was a white string on his head from the tuque meaning his hair should also be found on Kasakura's tuque. Kasakura confesses and reveals that her boyfriend had been cheating on her for the past two years and she killed him in vengeance.

Conan, Kogoro, and Ran pass by a woman named Kyouko Takahata who passes out upon receiving a phone call that her brother-in-law, Itsurou Soejima was found dead in her home. They head to her house along with the police to discover that the drunk Soejima died when he fired a shotgun toward the ceiling causing a chandelier to fall on top of him. The police conclude it was suicide, however Conan believes it was a carefully planned murder. Conan investigates and discovers that in the past year, Takahata was involved in all the alcoholism incidents that almost resulted in Soejima's death. After gathering the evidence, Conan tranquilizes Kogoro to reveal his deductions. Conan reveals that Takahata called Soejima to her home and had prepared the alcohol and shotgun to tempt Soejima, who is a recovering alcoholic.

The Detective Boys hear a rumor from a classmate about a warehouse with a treasure that can instantly appear and disappear. Before heading to the warehouse to investigate, the Detective Boys drop by Conan's house where they run into an unknown person unbeknownst to Conan. During the warehouse investigation, Conan notes there are fresh adult-sized footprints even though the warehouse has been locked up for years and that they lead up to an abacus with an odd number of beads. Conan decides to look through the warehouse by climbing a tree and sees a pile of treasure. The Detective Boys reenter the warehouse from the front entrance only to discover the warehouse it empty again. While Conan deduces that there might be a mechanism in the roof or in the floor, the Detective Boys prove him wrong declaring that the distance between the window and the roof is two meters from the outside and inside and that the markers they placed on the floors did not change.

Conan investigates and realizes the warehouse is designed by Samizu Kichiemon (三水 吉右衛門) and that the abacus is the switch that will reveal the secret room. The Detective Boys and Conan have the owner of the warehouse call the police before revealing their deductions. When the police arrive, the Detective Boys explain that the warehouse has a low ceiling which was concealed by the interior design of the warehouse. A fake window was installed inside the warehouse to mimic the distance between the window and the ceiling outside the warehouse. Conan then explains if the abacus is arranged as to display the Kanji Samizu (三水), the ceiling would lower revealing the secret room. After doing so, they discover a man in the room. They learn that the man was a serial robber and the treasure was all stolen good. Conan then reveals to the Detective Boys that he discovered Heiji had been giving them advice during the investigation and forces Heiji to come out of hiding.

After returning to Detective Mori's agency, Heiji asks them to help find Teruaki Kunisue, a sophomore at Teitan University who Heiji accidentally gave Kazuha's lucky charm to. They all head to Teitan University the next day only to find out that he has not been attending classes due to a broken wrist. Ran learns from Kazuha that she left a photo of Heiji in it and does not want Heiji to find out about the charm's contents. Later, Ran, Conan, Heiji, and Kazuha, go to a sports parlor where Teruaki was last spotted only to discover from the police that Teruaki has been assaulted by an unknown assailant. They are able to narrow down the suspects to three people since they were not in the bar-room during the time of the attack.

Conan and Heiji interrogate the three suspects to learn that they respectively attended a sumo match, a volleyball game, and a soccer game. Conan and Heiji deduce that Teruaki attended a baseball game and that one of the suspects must have also attended the same game. Conan and Heiji realize that the soccer game fan, Takuya Kyuma, had been using baseball terms to describe a soccer game meaning he is the culprit. They reveal that Kyuma attacked Teruaki for a baseball he got from a home run and reveal that the baseball is in his popcorn bag. Kyuma confesses and reveals his recently deceased girlfriend's wish was to receive a baseball hit from a home run. At the hospital, Teruaki decides to give Kyuma the baseball and drop the charges after hearing his story. Teruaki apologizes to Kazuha and tells her Heiji has her charm. Heiji finds the picture has been doodled on and misunderstands Kazuha's feelings for him and enrages him.

Conan, Kogoro, Ran, and Sonoko are at a tea house when a woman wearing gothic lolita fashion clothing enters the tea house, orders a glass of water, and leaves. Ten minutes later, a woman named Yuika Shoudou, arrives to the tea house where they learn that she was supposed to meet with the gothic girl from before. The four then leave to go shopping. On the way, a pair of thieves tries to steal their shopping bags by spilling ice cream on Ran and Sonoko but are foiled by Conan. The girls are forced to change in a public restroom where they find the gothic girl from before dead. The cell phone of the deceased, Mihiro Kuze, reveals she had been receiving phone calls from Shoudou. The police confirm with the waitress at the tea house that Kuze and Shoudou arrived ten minutes apart and with the public restroom thirty minutes away, removes Shoudou as a suspect.

The police investigate the glass the gothic girl was drinking which holds Kuze's fingerprints. At the ghotic lolita shop where Kuze bought her clothes. The employee there revealed that the gothic clothes were sold in pairs causing Conan to receive an epiphany on Shoudou's allibi. Conan tranquilizes Kogoro and reveals that the gothic girl that entered the tea house was Shoudou and that the glass was pre-prepared with Kuze's fingerprints. As evidence, Conan reveals that the wound on Shoudou's hand reveals that she was scratched by Kuze while strangling her and that her blood must be in the public restroom somewhere. Soon after, Takagi calls confirming that a luminol reaction was positive in one of the stalls and that a test will prove whose blood it is. Shoudou confesses and reveals that Kuze caused her to lose her boyfriend, housing, job, and friends as Kuze wanted Shoudou all to herself.

The Detective Boys attend a firefly festival to commemorate a shinto shrine in a village. The truck soon arrives with the fireflies and they are released into the fields. Later one of the truck drivers, Tokurou Nakamine, is found murdered and three of the villagers are the prime suspects. Conan notices a flashlight Genta found inside the truck and realizes who the murderer is. Using Agasa, Conan reveals the second truck driver, Shuchirou Tarumi, to be the murderer. Conan reveals that Tarumi murdered Nakamine in a desolated location near the village before turning the truck around and meeting with the other villagers. As evidence, Conan reveals the flashlight Genta found was actually a dictation machine with Nakamine's voice recorded on it. Tarumi takes Haibara hostage and attempts to flee but is eventually apprehended. Conan reveals that Tarumi's was tried of being blackmailed by for embezzling money from the firefly project and Nakamine's company and thus motivated his murder.

The Detective Boys run into a strange man named Kyouzou Daita who invites them to a cake shop after they apprehended a thief who robbed him. While talking with him, Conan notices the man is acting strangely. That night, the Detective Boys confront him and reveal he plans to kill himself and make it look like an accident in order to use the insurance money to pay for his grand daughter's surgery. Daita confesses and reveals that after losing a winning lottery ticket, he contemplated suicide was his only option. Conan deduces that the lottery ticket is in his reading glasses case containing his after hearing his story. Daita, happy to have the money for the surgery, jokingly tells the Detective Boys he also thought of robbing a bank causing the Detective Boys to discuss the fact that a man resembling Shuichi Akai's description was at the bank.

The man explains he was knocked unconscious in the bathroom and found himself like that and that the bomber threatened that if anyone leaves the floor or calls the police, the bomber will detonate the bombs on that floor. He discloses the bomber's demands, to find the sender of thirteen red shirts. Meanwhile, Jodie has been searching for evidence of Akai in the department store. While Conan and Kogoro investigate, Conan discovers from the receipt that the shirts were bought on different days but always at 12:28 and that there are creases on the thirteen red shirts. At the same time, the Black Organization waits outside the department store with snipers waiting for Akai. Gin holds a gun to Kir's head explaining that if Akai is alive, he will kill her.

Conan arranges the red shirts in the order they were sent and folds them along the creases and deduces that the way the shirts were folded reveal a code. Elsewhere, Jodie spots Akai is on the floor where the bombing incident is taking place. Conan uses the cashier room's computer in order to search for a disaster that occurred in a snowy mountain on December 28. Okiya, who happens to be on the same floor, examines the red shirt and concludes the sender is related to a disaster that occurred on a snowy mountain and smiles slyly when he notices Akai in the crowd. Conan tranquilizes Kogoro and discloses that the bomber's behavior is inconsistent; He was desperate to search for the sender of the red shirts, yet he found the time to kidnap and strap a bomb onto the man. Conan then declares that the man strapped with the bombs is actually the bomber.

Conan explains it would be impossible to always have a shirt bought on 12:28 for all thirteen days and reveals the sender to be the cashier, Mai Seta. Seta reveals that the bomber murdered her father thirteen years ago in order to hide the fact he was embezzling money from her father's company. Conan reveals that the shirts creases are flag signals conveying the message "I saw you burying it". The bomber denies the murder until Conan discloses that the body must be near the cabin since the bomber was a novice at mountaineering. The bomber confesses and explains he wanted the best for his son to stop him from running away from home. Seta asks Conan how he knew it was related to the mountains to which Kogoro answers by reading the deductions he received from a cellphone text message. Conan and Ran trace the call to a man who explains he did not send the message and reveals a man resembling Akai was the one who gave him the phone.

Kogoro, Ran, and Conan are invited to comedian Asako Fujimori's birthday party, even though Kogoro failed to find her stalker. When they arrive, they discover that Fujimori has stabbed a man in a zombie mask. They presume that the zombie is Fujimori's stalker, but discover that it is Jiro Imaoka, Fujimori's partner in her comedic career. While investigating, Kogoro deduces that Imaoka wanted to scare Fujimori to worsen her heart condition and force her to retire as his comedic partner and concludes the murder to be self defense. Conan's investigation leads him to believe Fujimori made up the stalker in order to murder Imaoka. He tranquilizes Kogoro and reveals that Fujimori and Imaoka met at a nearby park, evidenced by the cockleburs found on them. Fujimori then pretended to lose her key and faked a heart attack forcing Imaoka to enter through the apartment's balcony to retrieve her heart medication. Fujimori, enters her apartment before Imaoka does and murders him.

Kobayashi insists on escorting the Detective Boys to the fireworks festival after hearing about a series recent robberies. Kobayashi becomes lost on the way when they decide to take a shortcut and witnesses a feud between two people in an alleyway which results in one of them being stabbed to death. At the police station, Shiratori questions Kobayashi about the murder of the woman named Akira Sumida. Kobayashi explains she heard a female voice threatening to kill the other in the midst of the argument. She adds on that the culprit was likely female due to her breasts and she saw a truck with the partially covered number 09 across the alley. Kobayashi leaves to go to the washroom when she overhears some officers mentioning how Shiratori may be dating Kobayashi only because she resembles Sato and is heartbroken.

Shiratori has Kobayashi listen to the three suspect's voices and has determined none of them was the voice that shouted out and storms out of the police station. Haibara explains Kobayashi must have seen Sato and heard the rumors that Shiratori is only settling for Kobayashi in place of Sato. Shiratori attempts to rectify the misunderstanding and confronts Kobayashi revealing they met many years ago in a bookstore when confronting a pair of thieves. Kobayashi is unable to remember the event and replies it must have been Sato. Later that night at the school, Kobayashi receives a phone call asking to meet her at the music room when a presence behind her shocks her.

Kobayashi enters the music room where the culprit proceeds to attack her. However, she manages to incapacitate the culprit with a suplex and is revealed to be Sato in disguise. The Detective Boys and Shiratori appear revealing Sato replaced Kobayashi in the hallway and names the culprit to be Ryuusuke Kodama. The Detective Boys reveal that Kobayashi's testimony was correct and that she mistook Kodama to be a woman in the alley due to his long hair and the position of his arm making him seem as if he had breasts. Conan explains the woman's voice that was heard belonged to the victim, and that 09 was actually OS and stood for the first two letters of Osaka Nico Nico transportation. Shiratori reveals that they questioned the truck driver who saw the victim and Kodama entering the alley. Kodama confesses and explains that Sumida planned to kill Kodama to receive money from his life insurance to settle his debt and murdered her in self-defense.

Jirokichi stakes the key into the wall and awaits for Kid's arrival. Kid causes a blackout and the timed explosives destroys the windows causing strong winds to rush inside the shrine. While the Detective Boys protect the pedestals, the center pillar is heard opening. When electricity is restored, they discover Kirin's horn is missing, Conan is knocked out by a taser, and cards signed by Kid attached to all four pedestals. Jirokichi reveals that the shrine had been secretly enforced with steel and an alarm would sound if Kid had escaped through the door and proclaims Kid must be in disguise and inside the shrine; The suspects are Jirokichi, Ginzo Nakamori, or one of the three reporters. Haibara deduces from the inscribed message on the pillar that there is another method to open the pillars without the use of the keys. From the colors and Kanji on the pedestals, Haibara discerns they represent the Four Symbols: the Vermilion Bird, White Tiger, Black Tortoise, and Azure Dragon.

The Detective Boys discover Conan is feigning to be in an unconscious state to deduce Kid's motive for stunning him. The Detective Boys inform Conan what occurred during the black out allowing him to deduce who Kid is disguised as. Conan has Haibara reveal to the adults that Kid manipulated the Detective Boys, unknowingly, into opening the center pillar by having them lean on the pedestals. Haibara explains that the Four Symbols each represent a season; The inscribed writing in the pillar describes going with the flow, and when the pedestals are pushed in the order of Spring, Summer, Autumn, and Winter, the center pillar opens. She reveals that Nakamori had asked them to protect the pedestals in exactly the same order and reveals Nakamori to be Kid. Haibara discerns the cards were attached to the back of the Detective Boy's custom made anoraks disproving Kid had an accomplice.