The Detective Boys are stranded on a mountain when Agasa's car breaks down. Seeking shelter from the rain they come across a villa where piano music was heard and enter the house when their calls are unanswered. Inside, they explore and discover a diary on the table confessing to a plan of a kidnapping and murdering a boy; a blackout then occurs due to the storm. They find a small coffin planned for the murder and realize its empty and the possibility the boy is still alive. At that moment, piano music is heard again. Conan assures them it will be safe to search the house as the culprit is playing the piano. Ayumi wanders off on her own and finds a photo of a family and a room with water leaking out of it.

Realizing the piano playing they hear is a recording, they enter the piano room. Conan notices the piano chair was set to a child's height and deduces where the boy is. He has the Detective Boys sing a song in the piano room and catches the boy watching them and befriends him. The boy, Keita Onoda, is a piano prodigy to which the kidnapper abducted to allow his daughter to win a piano competition. Conan also reveals the dairy entry is out of order due to Keita's tampering and that the kidnapper felt increasingly guilty as the days went on. After reading the last page in the dairy, they realize the kidnapper plans to suicide in the bathroom and manage to save him. In the aftermath, Keita's mother does not push charges due to Keita's defense. The kidnapper's daughter meanwhile, revealed she skipped the piano competition as she was worried about Keita's disappearance.

Kogoro, Ran, and Conan find a cat belonging to a rich British woman who offers to pay their expenses on a trip to London so Kogoro may share his detective stories with her friends. To get past airport security, Haibara offers Conan two antidotes to the APTX 4869 for the trip and back. At the Holmes museum, Ran calls Shinichi asking him if he wants a souvenir from London. His weak reaction causes Ran to angrily hang up. Outside the museum, a kid named Apollo Glass asks to see Sherlock Holmes to solve a code that will prevent a person from being murdered. Conan offers to solve the riddle by posing as Holme's apprentice. Apollo reveals a strange man gave him a note containing seven coded riddles, declaring someone in London will die if it is left unsolved. They learn from the police that many children received the same code which Conan speculates to mean a large number of people will die. Conan and Agasa separate from the group as they attempt to decode the riddles.

Ran, feeling upset as she believes Shinichi does not share her feelings, is confided by Apollo's sister, pro tennis player Minerva Glass. Minerva then parts ways with Ran advising her love is zero and would never amount to anything no matter the effort. Ran calls Shinichi for advice on the riddles. Conan, tells Ran the first riddle "A rolling bell rises me", refers to Big Ben and accidentally reveals he is in London. Realizing Ran will discover Conan's true identity if she finds him, Conan and Agasa flee from her. Conan becomes cornered in a phone booth and is forced to take the antidote to the APTX 4869 for the return trip and confronts Ran as Shinichi. Ran confesses her pain of liking Shinichi who is indifferent to her feelings and runs away as he pursues her.

The next day, the police reveal the identity of the man who created the note, Sabara Hades. Kogoro and Ran decode the riddle "My portion is like a chilled boiled egg like a corpse" which refers to City Hall. There, they find many dolls with Mazarin Stone written on their shirts where when beheaded, reveals the letter "T". The riddle "I finished up with a whole pickle" refers to 30 St Mary Axe where scratched up pens labeled as Dancing Men reveal the letter "N". Ran and Kogoro revisit Big Ben following the riddle "It rings again for my hatred" and find an arrow pointing to a drain where The Valley of Fear of fear is inscribed. They deduce something had been sunk in the river, and find a drain cover with the letter "A". Apollo leads the two to the next riddle, "Now I remember to ask a cake to celebrate in advance" referring to St Bride's Church where they find letters entitled A Scandal in Bohemia. Soaking the letter in water reveals the letter "S".

Shinichi has returned to Conan again. However Haibara had only given him two pills, he will have to figure something out. Gradually deciphering the note handed out by the criminal, Conan discovers that the place where he plans to attack will be at Wimbledon, where Minerva Glass is supposed to be playing. When they reach the stadium, the criminal has already entered, and since they do not have tickets, they stay outside. However, they can watch the game from a screen that is located outside of Wimbledon. Minerva appears to be losing.

Conan notices Minerva's serves are braille for "help" and convinces Apollo to lend him his ticket in order to enter Centre Court to locate Hades. From the stands, Conan conveys to Minerva he is Holme's apprentice and he will help her. In the same manner, Minerva relays the message "Game Set Death Mom" revealing that at the end of the finals, her mother, Juno Glass, will die. Conan suspects that the teddy bear Juno received contains a bomb and the detonator is with Hades who is presumed to be watching her from across the stands with a video camera. Realizing it would be impossible to remove the bomb without Hades noticing, Conan opts to search for the criminal and asks Minerva to stall the match as long as possible.

Conan locates Hades during Minerva's rally with her opponent and proceeds to his location. He meets his parents on the way who gives him the tickets needed to enter the stands where Hades is located. Yusaku Kudo explains that during a tennis match, the heads of the fans would follow the ball while Hades would continuously look onwards at Juno. With Minerva's help, Conan is able to apprehend Hades who is taken into custody. After Minerva wins the championships, Ran meets with her and tells her Shinichi confessed to her; proclaiming that while love is zero, zero is also a starting point. Conan meanwhile, is given an antidote for the APTX 4869, by his parents for the return trip to Japan.

The Detective Boys sneak into an abandoned building that due to be demolished to play hide and seek. While playing Genta hears someone tapping a 2-5-2 code which is used in Japan to call for help. They find two construction workers who claim to be surveying the area before destroying the building by implosion. Conan quickly deduces they are confining a person in the building due to regulations preventing the building they are in to be imploded. The criminals, realizing they have been figured out, seal up the building and chase after the kids. Conan is knocked out by his rebounding soccer ball and Ai is captured. The criminals prevent the remaining Detective Boys from calling the police by threatening to kill Conan and Ai.

Mitsuhiko, Ayumi, and Genta hide in the lockers where the criminals confine their hostages. The criminals attempt to call the hostage's home for ransom but is answered by a young man. Concluding their plan to be a failure, they opt to set the building ablaze to hide the evidence. Conan communicates to the Detective Boys by tapping his detective badge, and orders them to call their cellphones to lure the criminals out of the room. After doing so, Conan incapacitates one of the criminals and tricks the other one into fleeing the building. The second criminal is then knocked out by Subaru Okiya who picks up the kids and reveals the kidnappe to be Agasa. Subaru reveals he deduced Agasa's situation from observing the house and receiving the ransom phone call and had tracked the kids down using Conan's spare glasses. Meanwhile, Agasa reveals he tapped the 2-5-2 purely by coincidence while hoping others would notice.

Chiba searches the storage room of Teitan Elementary for a thirteen-year-old VHS tape from his childhood love, Naeko Miike, which contains the reply to his love letter. At the same time, the Detective Boys are sent to the archives to search for a tape for their teacher. Chiba reveals to them that he received a phone call from Naeko Miike asking him if he has seen the tape, prompting him to resume his search for it. Conan deduces the tape contains the video Chiba and Naeko filmed years ago and finds the tape has been recorded over. He realizes Chiba was pron to sweaty hands and reveals Naeko wrote on the side the tape with red permanent markers which reveal she reciprocated Chiba's feelings. Chiba attends the school reunion only to find out Naeko did not attend.

Kogoro attends his alma mater and takes Conan, Ran, and Sonoko with him. A university student named Sonsaku Tsujiei asks Ran if she could examine how realistic their corpse is and guides her along with Conan and Sonoko through a haunted house production hosted by Tsujiei and his three friends. Inside the set, Anna Tadami dies after convulsing on a table. The police conclude it to be suicide after finding a cyanide capsule in her mouth and her past obsession with death. However, Conan points out that marks on the victim's face revealed an unknown assailant forced Tadami to bite into the capsule allowing the police to consider the possibility of murder.

Conan investigates the scene and deduces Tadami was already dead before they arrived in the room and that the culprit feigned her convulsion in order to fake the time of death. He tranquilizes Sonoko and explains his deductions to the police revealing the culprit went under the table and used his feet in place of Tadami's which caused the convulsion. He declares Tsujiei as the culprit, evidenced by Tsujiei's toe nails which were painted red to match Tadami's feet. Tsujiei confesses and reveals Tadami encouraged their terminally ill friend into suicide a month ago because she wanted to see a person die.

The Phantom Thief Kid sends a notice to Jirokichi Suzuki announcing he plans to return three stolen artifacts belonging to Sakamoto Ryōma: the letter, a cup with Ryōma's blood, and the pistol; during the Ryōma exhibition. Jirokichi persuades the owner of Ryōma's items, Shishihiko Tarumi, to host the exhibition in his museum while he sets up a trap to capture Kid. Sonoko, Ran, and Conan visit Jirokichi for more details. While there, they receive a second notice from Kid who announces his heist will take place the following day and quotes Ryōma on his plans to clean up. Conan deduces Kid ascertained the day due to the forecasted rain and advises Jirokichi to install metal detectors in the museum.

On the day of the heist, Conan is confronted by Kid in the bathroom stalls who reveals he was able to bypass the metal detectors by removing the lead from the pistol. As Kid leaves, Conan overhears Tarumi and his appraiser hoping Kid succeeds in his plot. Kid appears at the announced time and publicly claims he is cleaning up before setting off the fire sprinklers; he blends into the crowd who are also soaked from the rain and makes his escape. The water washes off the description plates in the museum revealing messages from Kid detailing the items in the Ryōma exhibition are fake and how Tarumi had been creating forgeries and selling them to the black market. This is confirmed when they discover many identical copies of the letter, cup, and pistol returned by Kid. As evidence, the blood on the cup is revealed to belong to Tarumi's appraiser and partner in crime.

Conan, Ran, Sonoko and the Detective Boys are invited to a small island resort for diving lessons. While exploring the island, they find a filming crew lead and directed by Yuuya Miyasaka, an actor who lost his fame due to assault causing the drama he starred in to cancel. When the weather turns bad, they all return to the resort. Later, Miyasaka is found dead in his room. The resort staff, film crew excluding Miki Kitagawa, and Conan's company meet in the lobby to discuss the identity of the murderer. Due to the rooms having an automatic lock when closed, they conclude Miyasaka had let the perpetrator into his room and suspects it to be the work of one of the crew members.

Kitagawa returns to the lobby and exclaims she saw Shingo Takayama, the cameraman, fleeing from the resort. Led by Kitagawa, they find Takayama's body off a cliff. After investigating Miyasaka's body and the camera which recorded the first instance the body was found, Conan realizes who the culprit. After tranquilizing and impersonating Sonoko, he reveals Miki Kitagawa as the culprit. He reveals that the instance they found Miyasaka, he was feigning death as a prank. After everyone except Kitagawa goes to the lobby, she committed the murder and exchanged the knife, evidenced by the stains on the knife's handle. She then proceeded to murder Takayama who was an accomplice to Miyakasa's prank to hide her alibi. Kitagawa confesses and reveals her as vengeance after her first big role as an actor was denied after Miyakasa caused the show to drama to be canceled.

For the past few days, Ayumi has been practicing her baton throws in the local park and has noticed a strange man watching her. One day while accompanied with her friends, the strange man is found dead. The police conclude it to be an accidental death after he fell from climbing the infrastructure. Since the victim was found with a cut on his face on the 6 of the floral clock, they presume the death to be at 4:30. Conan realizes the victim, Shousaku Yoda, is not the strange man and that the murderer impersonated him to have the Detective Boys become witnesses to his death. The police investigate Kyouichirou Kawaguchi, a man who bears a grudge against the victim, but has an alibi for the presumed time of death. After Conan investigates, he gathers the police and reveals Yoda's time of death was false. Kawaguchi murdered Yoda on the 6 but climbed across the clock to scratch his face on the 12.

A threatening letter signed "the Guardian of Time" warns that Rukako Hoshina, the mistress of a large mansion with a clock tower, will be murdered during her birthday party at 6:00PM. Kogoro and Conan goes to protect her but fails. It appears that the culprit stabbed her with an ice pick and fled from the balcony, but shoe prints and the murder weapon are never found. According to witness testimonies, the culprit is in a dress who moved nimbly, yet is plump and of a large build, yet no one in the party matches the description.

Conan deduces that Hoshina was stabbed with an umbrella, which fitted the description perfectly. A contraption on the mansion's clock tower set up by the culprit dragged the umbrella away and out of sight when it hit 6:00. The culprit is one of the party guests, Teigo Karube, who had designed this mansion and lost his clock technician friend four years ago. He reveals that the mistress treated the clock technician like trash and even threw away his friend's beloved clock, so he killed her in order to avenge his friend.

Ran, Sonoko, and Conan are at a yoga weight-lost resort when one of its customers, Atsuko Degawa, dies from poison found in her food. Originally deduced to be a suicide, Conan reveals the culprit as the resort's owner, Tsukiko Satoyama, who had poison laced on the plastic wrap which mixed with Degawa's food when it was re-heated in the microwave. After finding the poisoned plastic wrap on her dog, Satoyama confesses and reveals Degawa's negative reviews caused her parent's business to shut down and as a result, had her parents commit suicide.

Kogoro is asked to star in an educational television program. Once there, he is introduced to guest stars and studio members. Noburo Kimijima, the leading figure of Enka, has his priceless vase stolen during rehearsal. They deduce the culprit is still inside the studio room.

After failing to find the vase in possible hiding spots, Conan realizes the vase has been smashed and reveals it is hidden inside the fanny pack of Kimijima's disciple, Shinobu Oki. Conan deduces her motive and has the guest star appraiser reveal the vase was a counterfeit and that Oki most likely destroyed it to prevent Kimijima from being humiliated on television. Oki confesses and reveals Kimijima's wife's dying wish was to prevent Kimijima from learning about the vase's real value. Kimijima accepts Oki's good intentions and reveals he made a deal with a producer who will help start Oki's debut as a singer.

Kogoro, Ran, and Conan are walking when they witness a car attempting to kill a girl and her chauffeur. After saving the two, they learn that the girl, Kaede Nakakita, is an adopted child of a wealthy man named Ouzaburou Katayose. Katayose invites the three to his estate to express his gratitude towards them. As Conan explores the estate with Nakakita, he finds evidence that someone wants to kill her and deduces the culprit is either Katayose's son, Ogito Katayose, or his daughter, Nobue Katayose who are after the inheritance. Later, Katayose is found dead after consuming poison in his tea. The chauffeur Eiko Suzuka, then reveals Katayose's will detailing the location of his red leaf treasure.

Nobue is found dead with a poisoned arrow in her back while holding a clean arrow in her hand. Ogito's crossbow is found near the scene leading the police to suspect him. Later, Ogito falls down a cliff due to being shocked by an electric fence. Conan, realizing how the events transpired, tranquilizes Kogoro and reveals how the three died. Katayose poisoned himself and hoped to frame his children in order to protect Nakakita from their greed. Nobue, seeking to increase her inheritance, set up the crossbow and held an arrow in her hand to frame Ogito for attempted murder, but was instead murdered by Ogito. Ogito meanwhile, figured out the location of the treasure which is placed inside a cross made of metal rods. As he attempted to remove the treasure, Suzuka re-activated the electric fence which unintentionally resulted in his death. As for the treasure, it reveals Katayose leaves his inheritance to Nakakita who is actually his blood-related granddaughter from his former love.

Kogoro and Conan eat out at a ramen restaurant. Tokumori Saizu, the president of a real estate company, dies while beginning his meal due to poison. The police arrive and order Kogoro, Conan, and three suspects out of the shop while they investigate.

The police reveal poison was only found on the victim's left thumb and forefinger causing them to be dumbfounded on how the poison was applied. Conan asks the police what possessions the suspects have and eventually realizes how Saizu was killed. He tranquilizes Kogoro and reveals Atsushi Tanaka, Saizu's barber, as the culprit. He explains how poison is applied on the rim of the victim's glasses during his haircut. When Saizu cleaned his glasses due to condensation, the poison got onto his hand and into his mouth when he broke the chopsticks. After Saizu died, Tanaka exchanged his glasses with the victim's to hide the evidence. Tanaka confesses and reveals he murdered Saizu in the restaurant in order to have it close down and remodeled for greater success. A month later, the ramen restaurant reopens in a new location and becomes popular after changing its slogan.

Ran, Sonoko, and Conan head to a hotel for a cake buffet. On the way there, a molester is stopped by Masumi Sera, who befriends the group. At the hotel, Teigu Usumi killed after being thrown off the hotel while fashioned as a suicide. The police arrive and reveal the annex where the victim vandalized the security camera is the only blind spot in the hotel and most likely the murder location. There, they discover a wheelchair attached to a long fishing line.

After investigating the room, Masumi declares the culprit to be Toshiko Hirukawa as she lied about the elevator usage to Conan. She reveals Hirukawa got Usumi drunk, placed him on the wheelchair, and used a system of strings connected to the elevator to throw him out the window. However, re-acting the scene fails, until Conan voices his deductions over the phone as Shinichi revealing the paint cans were placed out of the window to tilt the wheelchair. Hirikawa confesses and reveals her father begged Usumi to apologize for scamming her mother but was refused. Afterwards, her father committed suicide after her mother died from shock. In the aftermath, Usumi's hidden bank account was found and the transactions to it allowed the police to apprehend the scam group. Masumi later enrolls into Ran and Sonoko's classroom.

Heiji explains Kazuha went to Wakamatsu's home in Osaka per the letter's instructions where she finds a disguised person with the word "EYE" carved into the bathroom tiles. The person causes a blackout, sneaks away, and the carved words disappear.

The police arrive and their investigations reveal the baumkuchen was cut evenly into eight pieces and that only one of the piece was poisoned. As police interviews the suspects while the widow, Serika Wakamatsu, is excluded since she was never close to the baumkuchen tray. Meanwhile, the police detectives in Nagano reveal to Heiji that Wakamatsu's killer reorganized the bathroom tiles to hide the dying message; The tiles used the crazy diamonds optical illusion giving the impression that it could not be rearranged without breaking the pattern. When arranged back to normal, the message reads "SON" indicating Ikuro was Wakamatsu's killer.

Conan and Heiji resume their investigation while Ran and Kazuha gossip about Shinichi's confession towards Ran. Conan and Heiji discover powdered poison on Ikuro's doorknob and Serika's slippers; the evidence indicates her as Ikuro's murderer. The two confront Serika whom is found dead in her office from cyanide poisoning. Wakamatsu's secretary, Satake Yoshimi, reveals that per Serika's will, a letter of confession to Wakamatsu's murder is to be given to the police upon her death; the letter confirms Ikuro was the murderer and Serika's role in hiding the dying message.

Conan and Heiji's investigation leads them to realize how Ikuro and Serika were murdered. They reveal that when two pieces of the baumkuchen were left, they were rearranged using the Jastrow illusion and applied poison to the seemingly larger piece. For Serika's murder, the same culprit used the Gestaltzerfall phenomenon while she was signing contracts. This caused her to forget how to write the Waka (若) kanji forcing her to open a dictionary to the Wa (わ) pages where poison was applied. They reveal the culprit to be Satake, evidenced by the shine on her bronze watch due to a chemical reaction with cyanide. Satake confesses to the murders and explains it was to avenge Wakamatsu who was secretly her father. In the aftermath, Kazuha attempts to confess her feelings to Heiji but fails when he leaves partway.

The Detective Boys are cooking curry at Agasa's home while Conan is asked to appraise an antique vase. The kids later leave to buy curry ingredient and return to find Agasa unconscious and Ayumi missing. The kidnappers send a message demanding them to look for a cat in return for Ayumi. The kidnappers send a second message saying they found their cat and detailing Ayumi's location. After rescuing Ayumi, who was rolled up in Agasa's antique rug, the Detective Boys attempt to deduce the kidnappers' motive.

Conan realizes the kidnappers invaded Agasa's home too quickly and deduces they have visited recently; Agasa reveals three pairs of customers have expressed interest in the vase. Realizing the culprits watched Agasa's online video of the vase, Conan finds the picture of the missing cat online and realizes the cat was a red hering. Conan realizes the culprits exchanged Agasa's rug with a fake and that the real rug is a valuable Persian rug. He deduces the culprits are knowledgeable about rugs and run a nearby carpet store since they had to disguise their voices. After finding an image of the culprit online, the Detective Boys confront the kidnappers, and have them convicted them based on Ayumi's earprint found on the real rug. Conan has Agasa's video erased, due to Haibara's appearance on it. Elsewhere, Masumi assists in deleting the same videos.

Through Sonoko's contacts, she invites Ran and Conan to attend the pre-opening of a chocolate restaurant managed by the famous chocolatier Yukihiko Tsujimoto. During the presentation, a fire ignites and Tsujimoto burns to death. After Conan investigates, he uses Sonoko to reveal the fire was caused by using a makeshift lithium–air battery; Salt water and the aluminum cups created static electricity which ignited the steel wool and alcoholic vapors. He reveals Mayuko Sakura, the victim's partner, to be the culprit, evidenced by the fact the water was not salted until the presentation began. Sakura confesses and reveals Tsujimoto manipulated her feelings for his own gain and intended to exile her after his success.

The Detective Boys discover officer Chiba's has been vandalized with a threatening word. Realizing is the culprit is the same person who has been on a vandalism spree that month, the Detective Boys push Chiba into investigating it with his first love, Naeko Miike. They investigate an underground parking lot where the vandalism occur; There, a rear-end collision is caused by the vandalism culprit. The police seal off the parking lot leaving three people as the suspects. During the investigation, a draft removes Naeko's hat revealing her face to Chiba.

Chiba is unable to recall Naeko's face though notes his familiarity. During the investigation, Conan realizes the culprit's motif and has the police let the suspects leave. During the night, the police set up an itasha to lure the culprit out, revealing the culprit to be Tokuko Shigei. Tokuko was vandalising cars with obstructions on their rear windows due to the trauma of her child being killed by a car of the same condition. Afterwards, Chiba remembers passing by Naeko but remains unsure of her identity.