Agasa takes the Detective Boys to his uncles house which has been abandoned fifty years ago for a treasure hunt he had set up. Conan finds a 1 yen coin and reveals to Agasa that those coins were not produced until forty years ago and that someone had been living in the abandoned house. Conan investigates and finds evidence that an old man who spent his spare time carving coins lived in the house. Conan notices that someone has drawn strange codes on objects throughout the house. The codes are symbols consisting of the moon, star, and sun. The Detective Boys manage to find their treasure and realize that someone had destroyed them all. Conan deduces that an unknown culprit entered the house in search of some kind of treasure and was angered when Agasa's riddles lead him to a box of toys. Conan and the Detective Boys gather all the objects in the house with the strange codes on them and attempts to solve it. Agasa reveals that his aunt was receiving letters in the same code and that he had Booker Kudo decipher the message; He also reveals that when his aunt began receiving those letters, someone was looking through her mail. Conan realizes the symbols refer to Hiragana and that the culprit who was looking through Agasa's aunt's mail is the one who destroyed the toys and is searching for the treasure in the house.

Conan matches the symbols to the Hiragana table and reveals that the symbols in the objects direct to other objects in the room. Conan notices that the objects conjoin in the center of room and realizes it refers to the chandelier. Conan matches the markings on the chandeliers which causes a stairway to the attic to appear. The Detective Boys find a skeleton of an elderly man in the attic. Conan reveals that man was the one who created the code and was sending the mail to Agasa's aunt. Conan finds a 20 dollar plate used for creating counterfeit money and explains that the man was hiding from the person who forced him to create plates. The culprit reveals himself and says that he had been searching the mansion for the plate for many years and attempts to steal it from them. Conan however apprehends the criminal and he is arrested afterwards.

The Detective Boys are in a puppeteer camping trip, where they are practicing for a school puppet play. At the same time, a serial killer has been spotted near the areas of the camp. While at the camp, the students disappear with their puppets, leaving the Detective Boys alone. Mitsuhiko assumes that their teacher is the serial killer. After they disspear, only Mitsuhiko remains alone. After being cornered by the teacher, Mitsuhiko finds out they decided to scare him for being bossy, by the suggestions of Genta and Ayumi. Mitsuhiko runs away angrily but runs into the serial killer. Conan manages to stop the serial killer and he is arrested. Later, Ayumi kisses Mitsuhiko for playing that mean joke on him.

Hattori Heiji, bringing along Kazuha, is hired by the rich Takeda family to investigate a series of suspicious suicides that has plagued their mansion in Tottori Prefecture. Along the way, he gets lost but runs into Robert Taylor, a lost American, and Kogoro, Ran, and Conan, who happen to be traveling to meet the same client for the same reason. After arriving at the mansion, they meet the Takeda family, consisting of Yuzo, Yoko, Ryuji, Nobukazu, Sae, Emi, Chie, and housekeeper Shioya. Yuzo explains to them of the “spider curse”; in ancient times, a beautiful woman morphed into a gigantic spider attempting to attack a traveler but was shot with burning arrows and retreated to the forest where it died. Misa and Kinuyo Takeda both hanged themselves, and 3 years before, Akio hung himself as well. All three deaths would be blamed on the spider demon. When dinner is finished, Nobukazu disappears, but is found in hanging in a locked room with his corpse entangled in a “spider‘s web.” Later that night, Kazuha finds a pearl on the ground outside and, unbeknowns to her, is being stalked by the killer.

Conan and Heiji investigate further into the ghastly death of Nobukazu as well as the suicides of Misa, Kinuyo, and Negishi. Nobukazu suffered a blow to the back of the head before he was killed. It is brought to light that Robert was involved in a rockslide accident but was nursed back to health by Misa; they communicated with Rōmaji, but after Robert left, Misa committed suicide, her mother, Kinuyo, followed suit. Misa was already facing depression because she had learn that she was not her father's daughter, shrouding her birth in mystery. At Misa's funeral, Ryuji expressed deeper emotions and cried profusely. Emi and Sae claim Robert killed Misa after wrote a letter telling her to die. Robert has an alibi for the crime as he drove to the mountains with Ran and Kazuha. Chie was alone in her room, and Yoko was bathing with her daughters. When Kazuha hasn't been seen for some time, the group finds her entangled in the spider’s web, severely injured but still alive. Heiji finds a stun gun in the incinerator, he and Conan find tiny holes in the window at the crime scene and fishing lines with hoops at each end, and Negishi and Nobukazu are believed to be drug dealers after cocaine is found in their puppets. Together, they realize who the killer is and how the murder was pulled off.

Conan tranquilizes Kogoro and cooperates with Heiji to shed light on the case. First, Misa and Kinuyo both committed suicide with Misa's being the source of the Tsuchigumo rumor and its supposed curse. Next, Misa’s real father is Ryuji, not Nobukazu. The conception was an arrangement between Ryuji and Kinuyo, because Nobukazu had been declared steril and Kinuyo desperately wanted a child. This is evidenced by Ryuji's emotions at Misa's funeral given that he is her actual father. Finally, the killer set up massive piles of fishing line and a noose that was connected to a car with string. Nobukazu was lured to the room under the promise of a fruitful drug deal and killed; A BB gun pellet was shot at the window to get Nobukazu to look out. When the killer drove away, the noose wraps around Nobukazu’s neck pulling him in the opposite direction. His head struck the central beam nearly killing him instantly. The string snaps causing his corpse to fall into the fishing line below in order to take revenge for Misa’s suicide as well to put blame on the spider curse. Robert is the murderer, he is revealed to have killed Negishi as well for making a rude comment about Misa, and attacked Kazuha because she found a BB gun pellet mistaking it for a pearl. As evidence, a few people knew about Nobukazu‘s death as he was entangled in strings and outside of those, one more person knew, the killer himself. Robert confesses how he was enraged how no one stopped Misa’s suicide. When he shows no mercy for attacking Kazuha, Heiji reveals it was his own message; Robert wrote “SHINE” as in ”the shine of his life.” “SHI-NE” in Japanese means “die.” Robert, completely devastated and regretting his actions, is arrested for the murders.

Kogoro is invited to an aquarium where an underwater play is to take place, A woman's dead body rises from the water when it's her cue to come out of a clam's shell in the play. Conan solves the case and the culprit reveals it was revenge for the murder of his wife and child.

Conan detects a change in Ran’s behavior and speculates that she may have something going on. Kogoro, on the other hand, takes them to his doctor Yoshiteru Araide’s house for a checkup. There, they meet the doctor, his wife Yoko, his mother Mitsu, and son, Tomoaki Araide, with who Ran seems smitten by. The maid, Hikaru, breaks a vase and is warned by Yoshiteru that she'll be fired if she does it again. During dinner, Yoshiteru takes a bath and a black out occurs and another vase breaks. Hikaru flips the breaker on, and she and Yoko find Yoshiteru dead with his electric razor in the bathtub. Alibis and suspect locations are checked but Conan can't bring himself to concentrate on the case as Tomoaki and Ran are seen drawing closer to each other.

Conan establishes that Yoshiteru was murdered and finds several clues missed by the police including a broken piece of a vase. Mitsu suffered a small cut and Hikaru burnt herself. Conan, through Kogoro, announces his experiment to solve the case, however, it is actually a trap to catch the killer, Yoko Araide. Conan deduces that Yoko flashed her pin light in Yoshiteru’s face so he wouldn't see her sliding the razor into the bathtub. Hikaru flipped the breaker back on, thus killing Yoshiteru, as planned by Yoko. Prior to the murder, Hikaru broke another vase and hid it out of fear of being fired. Mitsu stepped on a shard on the second floor, and Tomoaki was held by Ran during the situation, leaving Yoko the only one with ample opportunity to commit the murder. Yoko confesses that her friend Chaiki was married to Yoshiteru but committed suicide due to his infidelity. She would then marry him to exact her revenge. Conan requests Yoko to bend the truth to spare Hikaru from knowing she is the actual cause of her employer’s death. After the case, Ran asks Tomoaki for his sweater so she can knit a similar one for Shinichi.

Ran, Sonoko, and Conan are at the Tropical Land ice rink where they meet a group of people: Yasuharu Misawa, Izumi Sano, Yoriko Komatsu, Chihiro Itami, and Kunitomo Oda. Chihiro goes to the women's bathroom where she is being followed by a cloaked figure. A shotgun is forced into Chihiro’s mouth by the figure as she attempts to talk her way out of her situation. Moments later, the fireworks start and Sonoko finds Chihiro dead inside the bathroom stall. An “S” smeared in blood indicates that Izumi Sano is the killer but she has the alibi of being with Ran at the start of the fireworks. They find Chihiro’s phone in her pocket and when they try redialing the last number, it reveals the letters “K.I.X”.

Bloody marks are discovered at and near the crime scene. Conan puts Kogoro to sleep to reveal that the culprit imitated the fireworks noise by blowing into a 5 yen coin, making people believe the fireworks started early. The killer is revealed to be Izumi Sano and the ”S” is not the real code, but the “K.I.X.” was. Chihiro was killed instantly as she was shot through her heart. K.I.X is the special code for Kansai Int’l Airport, located in Izumisano, Japan. She wrote the “S” on the wall after killing Chihiro with her own shotgun, using reverse psychology as the basis of her methods. As evidence, the blades of Izumi’s skates have traces of Chihiro’s blood on them. Izumi confesses with revenge as her motive for a deceased friend whose fatal accident was really a suicide, caused by Chihiro’s lies. The next day, Ran receives a new phone from Shinichi in the mail.

Saizo Kano, known as the Organizer of Shadows, is shot to death by his subordinates, Sadao Kujirai, Korehisa Kanie, and Teruyoshi Kameda. In the present day, while celebrating their last heist on a luxury cruise ship, Kano’s crew is picked off one by one by a mysterious killer. The stakes are raised when Heiji is thrown into the Pacific Ocean while investigating and a bomb is discovered to be hidden on the ship. Is there something more sinister afloat, or has Kano returned from the dead to enact his vengeance 20 years later?

Richard is called to investigate a suspicious murder where three people admit to killing a man for hitting him on the head. His posture showed the death to be a heart attack. They are all actors in an actor studio, their boss was the manager. After seeing the evidence, they find out that all four of them have attacked him but not killed him. He was killed by his wife who stole his heart pills and he died of a heart attack.

On the way home from school, Conan and Haibara find Gin's Porsche 356 on the street and places a covert listening device in it. Conan hears that a Black Organization member codenamed Pisco is ordered to assassinate someone at a party hosted at Haido Hotel. Gin finds a strand of Haibara's hair in the car and manages to find the bug and destroys it; He realizes Haibara will be at the hotel and orders Pisco to kill her when he gets the chance. Conan and Haibara head to the hotel in order to capture Pisco. During a slide show, Pisco manages to murder his target, a lawyer named Shigehiko Nomiguchi, by causing a chandelier to fall onto of him.

Conan investigates and reveals to Haibara that the purple handkerchief will narrow down the suspects. Conan explains that the party is holding an event that is dedicated to a film known as "The Rainbow Handkerchief"; all the party guests are given various handkerchiefs with colors of the rainbow and that Pisco is one of the people in the purple handkerchief group. When the party guests rush out of the room in a panic, Haibara is knocked unconscious by Pisco and awakens in a locked wine storage room. Conan contacts Haibara through a communication device and tells her he had the police hold up the seven suspects which will buy her time to escape. Conan tells Haibara to drink some wine which when combined with her cold will negate the effects of to APTX 4869 and subsequently allowing her to regress back into her teenage self, Shiho Miyano. Meanwhile, Gin and Vodka enter the hotel and make their way to the storage room.

Haibara climbs to the top of the chimney only to be confronted by Gin and Vodka. Gin explains that he heard her breathing in the chimney while in the storage room and was waiting to ambush her on the roof. Gin prepares to kill her but is saved when Conan intervenes - changing his voice so they will not recognize him later; allowing Haibara to fall down the chimney and back into the storage room before becoming a child again. Pisco prepares to kill Haibara before he is interrupted by Conan who greets him as Kenzou Matsuyama the party guest. Conan reveals that Matsuyama lured Nomiguichi under the chandelier during the slide show and fired a silenced handgun at a fluorescence painted section of the chandelier causing it to kill Nomiguichi. Conan asks how Matsuyama was able to get a purple handkerchief after losing his but Matsuyama refuses to answer the question. Matsuyama's cigarette mixed with the wine in the storage room causes a fire and allows Conan and Haibara to escape. Gin confronts Matsuyama and explains that a journalist had taken a picture of Matsuyama committing the crime; To keep the Organization a secret, Gin kills Matsuyama. Shortly after, Gin and Vodka are seen with a third Black Organization member codenamed Vermouth.

Conan and the group go to a coffee shop. Nearby, two men are having a meeting. One of them gets up to go to the bathroom, and while he's gone, a truck slams into the coffee shop and smashes the other man who was still seated. Conan realizes it was a planned murder and finds evidence through the truck, and the man's cut.

Kogoro is invited by Yoshinori Kana to his home to investigate an unknown stalker harassing his wife, Misaki, who leaves mysterious gifts and letters. After meeting the others; Masayo Tokudaiji, Michel Anglade, and Hideki Kana, a blackout occurs during a party. Conan and Kogoro rush to Misaki’s aid, and they find her forcibly grabbed by who appears to be her stalker. The stalker jumps out the window and escapes. Conan realizes these occurrences are related to the song ”Nocturne of Red.” As the night progresses, Gerard meets an unfortunate end as a sword falls from the chandelier and impales him in the back.

The case is solved, the mysterious man was figured out to be a statue hanged by a fishing rod. The culprit was revealed to be the man's wife, who wanted to protect the company and her husband from a scandal. Afterwards, Conan gives Ran flowers. Ran interprets the flower's with the meaning Invincible and gets angry at Conan.

The Detective Boys are walking home one day when they discover two s shaped hooks and a ring with the initials M to A, a wedding ring. They decide to investigate seeing it as an S.O.S. After a false alarm, Conan realizes one of the person who answered the door was not the actual person. He tranquilizers the culprit and saves the woman who was tied up.

One day, The Detective Boys were bored so they picked up receipts in a convenience store to guess what the people are buying for dinner. George picks up a weird receipt with food items, a dust bin, a container, a handler light, rechargeable batteries, thin lytax gloves, and chlorine. Conan figures out the man is trying to make the same poisoned bait used to kill moles. After searching around town to the stores they visit, they find out the approximation of the man's house and begin searching for bikes with handler lights and no basket. After finding him and following him one night, they find out he was trying to poison a dog to death. His motive was to silence the vicious and loud dog so he may once again walk his favorite path in peace.

Kogorou, Ran, and Conan are invited by the hostess of a car accident charity named Shou Beniko. While driving, they find a message from the Phantom of the Cursed Masks who tells them they should not go. Once there, they find other famous celebrities; a baseball player, a prophet, a rockstar, and a man who lost his wife in a Hit and Run incident. The mansion they will be staying at is a huge mansion divided by the east and west side; and the only room connecting the two sides is the mask room, which is locked at midnight due to Shobel's mask. They were created by a famous man who lost everything and became engrossed in his masks; once he created 200 of them, he was found dead in his room surrounded with bloody masks. People who have owned his mask have suffered tragic fates. Shou who now owns all 200 masks has a priest place a seal on the curse, but the room will locked at midnight to prevent them from wandering. During their stay, Shou was murdered in a locked room with masks surrounding her and a dagger in her throat. Conan later figures out the trick and reveals the culprit. The culprit reveals that his mother was blamed for a hit and run incident and murdered by Shou, who then took fame and profit from her charity.

Kogoro, Ran, and Conan are driving by when an arrow almost hits Kogoro. Afterwards, they stay at a hotel when an actor is found dead with a bullet in his head and all the evidence suggests it is the work of an outsider.

Conan later solves the case by showing how the culprit tried to place false evidence to lure the police to think it was an outsider. He later shows that a gun was not used to shoot the bullet but an arrow was. The culprit is arrested and he reveals he wanted to write a perfect crime script that no one could solve. Afterwards, Kogoro is offered a chance to star in his own show but Ran forces him to drive away before a deal could be made.

Kogoro is invited to a house as to impress the client's mother who is a finance trader, simply a loaner. Later, loaner is murdered and with the clues, the suspects are her son, daughter, or maid. Conan manages to solve the case and reveals the television was used to create the gunshot noise.

Ran's strange behavior causes Conan to suspect that she knows his identity as Jimmy. Later on, the Detective Boys are taken by Agasa on a camping trip. The Detective Boys explore a cave only to find bank robbers hiding a dead body. Conan manages to hide the Detective Boys but is shot in the process. With the entrance guarded by the robbers, Conan, carried by George , leads the Detective Boys deeper into the cave to find another entrance. As they navigate through the cave, they come upon a monument of an egg with the message "Those who are lost in the dark, take your steps towards the path of the dragon, then you shall be showered by the light of happiness." Conan explains that the monument explains which of the five paths ahead shall lead them to the outside and passes out from his injury before he could point them to the right direction.

The Detective Boys realize that the riddle is a reference to shogi and that the dragon refers to a promoted rook. They take the direction a rook is placed on the shogi board and escape the cave. The robbers are then apprehended by the authorities and Conan is taken to a hospital. At the hospital, the nurse reveals to Conan's friends that they ran out of Conan's blood type. Ran allows them to use her blood for Conan's blood transfusion and subsequently reveals that she knows Conan is Jimmy. A few days after Conan's surgery, Conan decides to tell Ran his true identity as Jimmy . Later that night, Vi enters Conan's room and holds a gun towards him.

Vi reveals the gun was a fake and reminds Conan the threat that the Black Organization poses. Since Ran knows Conan's identity, hiding it from her would be cruel but telling her would endanger the lives of everyone around him. Vi gives Conan a third choice that can solve the problem. The next day, Conan attends Ran's play where a Ran and a mysterious black knight are the main characters. During the play a man named Kouhei Mazuda dies from potassium cyanide ingestion. Heiji, disguised as Jimmy , attempts to trick Ran but is discovered by Kirsten. After removing his disguise Heiji concludes that the suspects are Mazuda's friends and the drink vendor.

The police are unable to find the source of the poison from the drinks. As they are able to rule the death as a suicide, the black knight declares it was a murder and reveals his identity to be Jimmy. Jimmy reveals that the poison was placed in the ice cubes and that Mazuda had a habit of eating ice. He reveals the murderer to be Mazuda's friend, Mai Kougami. Jimmy explains that Mai kept the ice cubes in a little purse which was kept cool through dry ice. Mai says that she bought the same drink as Mazuda and that there was only a fifty percent chance that he would take the drink with the poisoned ice cubes. Jimmy explains she put ice cubes in both drinks and that after emptying her drink, she placed the poisoned ice cubes in her hood evidenced when a 10 yen coin undergoes a chemical reaction with contact to her hood. Mai confesses and explains that Mazuda murdered his patient in order to have his medical thesis published. Shinichi collapses after solving the case and wakes up and realizes he still retains he is still Shinichi and has not regressed back to Conan.

The next day, Shinichi takes Ran to a fancy restaurant in order to confess his love. While there, a party for game company chief executive Taiji Tatsumi is to take place. Those who will attend are Satoru Ooba, his girlfriend Sakurako Tatsumi, and a few other employees. Taiji steps into the elevator and Satoru, brandishing a gun by his side, sends the others away, keeping Sakurako by his side. Satoru kisses Sakurako, opens the elevator door, and brutally murders a terrified Taiji with a bullet into his skull. He then gives Sakurako a present and compliments her earrings saying they look like a pink pearl necklace. Shinichi runs off just as Taiji’s murder investigation begins. He instantly proclaims Satoru as the murderer but Sakurako defends him, adding on that no gun residue was found on him. The weapon was found on in the garbage. Shinichi asks Sakurako about the kiss with Satoru and realizes how Satoru executed Taiji's murder.

After checking the company's mascot, Shinichi confirms Satoru to be the murderer, thus locking the two in a game of cat and mouse. Shinichi reveals that Satoru suggested to Taiji to change clothes in the elevator where he murdered him. Satoru covered Sakurako’s ear and shot Taiji at the beginning of the party to mask the sound of the gun whilst kissing Sakurako with a silenced pistol, glove and plastic bag so his clothes would not be stained with gunpowder. He got rid of the gun by throwing it down the garbage chute while waiting for Sakurako who was in the bathroom. As evidence, the plastic bag was hid in a mascot costume and that it contains Satoru’s fingerprints; however, he counters stating that his co-workers also touched the plastic bag. Shinichi reveals that Satoru already confessed to the crime also since he said his girlfriend's earrings were pink yet color is not distinguishable in the dark and thus states that Satoru was with his girlfriend when the elevator doors opened. Satoru confesses and reveals that his father's company was destroyed by Taiji and prompted his father to suicide. Shinichi escapes to the bathroom and regresses back to Conan. Ran, completely devastated that Shinichi left to solve another case, has a few words with Conan and eats ice cream with him.