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.

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.

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 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.

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.

Kogoro, Ran, and Conan are invited to assist in a rooftop farm. Once there, they discover the elderly farmer, Takehiko Nakamura, dead from a head injury. The police are brought in and the other three farmers are interrogated for the death. Conan's discovers a shattered brick with a hole and discerning how Nakamura was murdered, tranquilizes Kogoro and reveals the farmer Marie Inoue to be the murderer. Conan reveals that she hung a brick on the handrail and concealed it with a towel and lured Nakamura to it with a phone call. When he was close enough, she pulled a rope connected to the brick hitting him on the forehead causing him to lose his balance and having him fall into the corner of the water tank. As evidence, Conan explains the towel's paint mark is from the handrail and that the rope must be in Inoue's home. Inoue confesses and reveals that Nakamura killed her crop which were grown from her father's final harvest.

Ran discovers a receipt for a necklace in Kogoro's wallet and discerns that he is going to give it to Eri as a birthday present. Ran decides to enter a raffle draw to win a luxury hotel trip for her parents and succeeds in winning the tickets. Eri reschedules to meet her client at the hotel upon hearing about the supposed necklace. Her client, Akiho Koukuba, enters Eri's room after getting into a fight with her husband, Takehiko Koukuba, and falls asleep. Eri arranges for Takehiko to retrieve his wife and leaves to eat dinner with her family. She returns to her room, disappointed by Kogoro's behavior and the lack of a present and opens a carbonated drink but is soaked by the can; After showering to wash off the drink, she returns and finds Akiho dead in her room.

That night, Conan realizes how the murder was done and who the culprit is. The next day, he drops a hint for Kogoro by spilling ketchup on a food cart which creates an evenly spaced ketchup stain on the floor, miming the victim's blood stain. Kogoro has the police gather the suspects and declares Takehiko to be the culprit. He reveals that Takehiko placed his toy cars under the bed legs allowing the bed to easily slide. They evidence it with Takehiko's statement, when he said that James Dean's car was a Porsche 911, but in reality it was a Porsche 550; revealing he used the 550 in the crime. Takehiko asks how would he know Eri was going to take a shower. Eri reveals that Takehiko filled her fridge with only carbonated drink and Takehiko knew that Alcohol would make one thirsty. As evidence, the murder weapon, the ashtray in Takehiko's room, should contain Akiho's blood. Takehiko confesses and reveals that Akiho threatened to kill him to inherit his money.

Agasa takes the Detective Boys to the house of a famous aquarium designer, Nishida. Kousuke Imura lets them into Nishida's home when Nishida does not answer the door. The Detective Boys find Nishida drowned in his bathtub. The police determine that Nishida died the night two days prior and from falling asleep in his bathtub due to alcohol consumption. Conan's disproves the theory explaining that the bathroom light was not on when they found him. The police investigate Imura's alibi which confirmed he was in Guam for the past two days at a shooting range. Conan investigates and realizing how the murder is done, impersonates Agasa's voice and declares Imura the murderer. He explains that Imura used the cooler from the shrimp's tank to fake the time of death, evidenced by the wet glue that has yet to dry on Nishida's fingertip and the dead shrimps in the same aquarium.

Kogoro is called to meet with Toshio Higashiyama at his company building and takes Ran and Conan with him. Upon entering the building, they are asked to call his sectional number, 423. After getting in contact with him on the phone, they witness the employee Fujihiko Takahaka, fall from the building to his death. The police are called to the scene and enter Takahaka's office discovering a typed suicide note. Conan notices the window is open, a dry spot over the ledge of the window, and a piece of a theatrical property was found on the body and gives Kogoro hints allowing him to deduce Takahaka's death. He reveals the prop is the one used in fictional children's show where when shot with a laser gun, deflates. The prop was used to keep Takahaka's inert body from falling out the window, and was deflated resulting in his death and allowing the culprit to establish an alibi.

Conan and Ran are on a train and are confronted by a pickpocket but is saved by an elderly man named Tokuma Norizuki. As the train passes Sugamo Station, they notice the police investigating something under the railway. Conan and Ran discover that a man named Kanemura, a local conartist, was killed by a head injury. Norizuki claims he witnessed Kanemura's boss, Takehiko Kiriya, committed the murder. Kiriya said he was called to the crime scene by Kanemura's friend and proclaims he is not the culprit. Conan asks Takagi to investigate on Norizuki and learns that Norizuki's girl friend, Mitsu, was a victim to their conartist group which resulted in her death. Ran is able to stop Norizuki from murdering Takeshi Motegi, Mitsu's conartist and the police arrive. For the previous murder, Conan reveals that Norizuki got off the train 15 minutes late, revealed by the exiting time on his smart card.

Sonoko takes Ran and Conan with her to cheer for her senior tennis player, Takao Goutou. Goutou collapses in the middle of the match due to poisoning and is rushed to the hospital. The ones who are suspected to have poisoned him are one of the two girls he is dating, and Sonoko who becomes the prime suspect when poison is found on her glove. Conan tranquilizes her and reveals the culprit to be the captain of the tennis team, Fumihiro Azuma. Conan explains Azuma high-fived Goutou with a poisoned glove and poisoned his hand; thus explaining why poison was found from Goutou's drink, towel, and Sonoko's glove. As a result, Goutou ingested the poison when he licked his fingers while changing the grip to his racquet. As evidence, Azuma's glove was found hidden in a tennis ball and poison was confirmed to be on it. Azuma confesses explaining Goutou injured him purposely to usurp his position in the competition and consequently made him lose his sponsors and scholarship.

Sumiko Kobayashi is called to be a jury for a murder Tadashi Ishigaki. Toshio Iwamatsu, a burglar who broke into Ishigaki's home, is held accounted for the murder and Eri Kisaki is assigned as his attorney and Reiko Kujo acts as the prosecutor. Kogoro, Ran, and Conan attend the hearing where Ishigaki's housemaid and brother-in-law deliver their testimonies of discovering the body. Unable to find the murder weapon, the court ends without a decision and will resume the day after. During the session, Sumiko notes aloud that the painting in Ishigaki's room is upside down prompting Kogoro and Conan to investigate the room. Inside the painting, they find a document stating Iwamatsu burrowed money from Ishigaki. Conan deduces the culprit took a document and placed the painting upside down in his rush and discovers that a vase in the room is missing after Ishigaki's murder.

Due to the housemaid's behavior, Conan pressures the housemaid about the vase. That night, Kogoro and Conan ambush her in the middle of returning the vase to the crime scene. The next day, court resumes and Reiko presents the documents pertaining Ishigaki's burrowed money and the murder weapon found in a distant pound. Eri calls the maid up as a witness who explains she found the vase at a garbage collection point. Eri then calls upon Kogoro whom Conan tranquilizes and reveals the culprit to be the brother-in-law, Tooru Tsukano. Conan explains that after Tsukano murdered Ishigaki, he took a document, hunt up the painting, and hid behind the door as Iwamatsu entered the room and knocks the vase to Tsukano's feet. Tsukano hides the knife and gloves inside the vase and leaves the vase at the garbage collection point and establish and alibi. He then afterwards placed the knife in the park and disposes the gloves he used to commit the murder.

Kogoro appears in a commercial to promote white chocolate for White Day and is invited to a chocolate company's party. Kogoro, Ran, and Conan attend and are introduced to the company presidents, Taruto Urai and his wife Hoshie Urai. During the party, Taruto dies from cyanide poisoning. Inspector Megure and his Officers are called to investigate the death. The investigation leads Hoshie to be the prime suspect. As she is taken away to be searched, Hoshie trips and falls on a table causing many lemon tea glasses to shatter. Meanwhile, evidence of a medicinal wafer containing poison is found in Urai's mouth suggesting suicide. Conan is ascertain Hoshie to be the culprit and investigates on how she delivered the poison to her husband.

Conan investigates and upon discovering the method, tranquilizers Kogoro and explains how Hoshie committed the murder. He explains the burn marks on Hoshie's napkin indicate cyanide was on the napkin and the poison was placed on a lemon slice. Conan elaborates explaining how Taruto was famously known to hate sour things, and had planned to surprise his guest by eating sour food with the use of synsepalum dulcificum. Upon testing if the synsepalum dulcificum was still in effect, Taruto ate the poisoned lemon slice. While down, Hoshie took the lemon and placed the medicinal wafer in her husband's mouth and hid the lemon slice among the others during her fall. Conan concludes that Hoshie's fingerprint and Taruto's saliva should be on the poisoned lemon slice. Hoshie confesses revealing her motive is revenge for her former boyfriend who Taruto pushed to suicide.