Shinichi Kudo uncovers a murderer along with the police at a party. Later, Shinichi and Ran Mouri take a trip together to an amusement park, where a man is murdered during a roller coaster ride. Shinichi deduces that the people in front and behind the victim are the suspects. Shortly after investigating the scene, he reveals who the murderer is in front of a crowd of people. After the case, Shinichi spots two suspicious black-clothed men. He decides to follow them and witnesses a deal taking place but is attacked from behind. The two men, intending to kill him, force him to swallow newly developed poison.
Shinichi turns into a 7 year old boy after being poisoned.
Shinichi is secretly in love with Ran and imagines them admitting their love for each other. Later as Shinichi parts from Ran at an amusement park to check on some suspicious activities, Ran feels like she's seeing Shinichi for the last time (which will happen to have been somewhat of a premonition).
The men in black poison Shinichi after he is discovered spying on them.
Shinichi and Ran are presented as childhood friends and are shown to share a strong bond. Many other important facts about the characters are revealed (such as Shinichi's usual involvement in the police affairs).
Shinichi wakes up as a young child due to the effect of the poison. After running into Professor Agasa he decides he must hide his identity or those men in black will come back to finish off those connected to him. Shinichi renamed "Conan Edogawa" is placed in the care of Ran and her father, Kogoro Mouri who owns a detective agency which may allow him to gather information on the men in black. Kogoro receives a case to find a man's kidnapped daughter, Akiko. Conan drops subtle hints for Kogoro to solve the case revealing Asao, the butler, to have kidnapped Akiko but then a phone call reveals that Akiko has been kidnapped again. Conan follows the clues from the phone call and is able to locate her. After arresting the kidnapper, Kogoro, happy to have solved a difficult case, allows Conan to stay.
Shinichi decides to hide his true identity, knowing the mysterious Men in Black would come back to kill him if they discovered he is still alive and begins to use the alias "Conan Edogawa". Shinichi begins to live Ran and her father.
Ran admits to Conan she is secretly in love with Shinichi.
Conan at school meets up with Ayumi Yoshida, Mitsuhiko Tsuburaya, and Genta Kojima. The three decide to follow Conan home and make him one of their friends. Later Pop Idol, Yoko Okino, arrives at the Mouri Detective Agency claiming that a man is stalking her. Once there, they find a man with a knife in his back, dead. The man is revealed to be Yoko's high school boyfriend, making Yoko one of the three suspects. Conan investigates and figures out the truth. He knocks Kogoro out by kicking a cigarette tray to his head and with his Voice-Changing Bowtie uses Kogoro's voice to reveal the truth of how the crime was done. That night, Conan gives Ran a call and with his bowtie, using Shinichi's voice. He tells Ran he is on a difficult case and will return when he solves it.
After a day at the art museum, the Conan and his friends find a piece of paper with symbols and the word "Oro" written on it. Conan believes that it is a treasure map after he discovers "Oro" means gold in Italian. Conan and the Detective Boys then go around Beika City looking for the symbols indicated on the piece of paper but then they run into the Mafia! How will they get out of this mess?
Conan runs into the two men in black from before on the Shinkansen bullet train. Upon investigating, he finds out they only resemble the two men. Using his new glasses and a bug, Conan overhears their conversation about a bomb in a black suitcase on board. Conan is able to narrow down the location of the suitcase leaving four suspects. He is able to figure out who has the bomb at the last moment and with his Power-Enhancing Kick Shoes invented by Agasa, Conan manages to kick it off the train just in time.
Ran is invited to a Valentine's party and Conan, jealously, follows her. The host, Katsuhiko Minagawa, falls dead from poisoning. Conan investigates and finds out that he was poisoned from the coffee served to the party guests. Conan uses his newly acquired Stun-Gun Wristwatch that shoots a tranquilizer dart to put Kogoro to sleep and with his Voice-Changing Bowtie, pretends to be Kogoro. Using Kogoro, Conan reveals the truth.
Once a month for the past two years, a surgeon named Masayuki Ogawa has received toys and money totaling up to 25 million yen anonymously. He asks for Kogoro's help to find whoever is sending them. With Conan's suggestion, they check Ogawa's history of operated patients. During the investigation Ran begins to suspect that Conan is really Shinichi. When Conan tries out a video game that Masayuki received, he realizes that it belonged to a child, named Tomoya Ogino, that died during an operation led by Ogawa three years ago. He realizes Ogawa's son, Yuta, may be in danger and the group sets out to rescue Yuta before anything happens. That night, Conan manages to deceive Ran about his identity by getting Agasa to call her as Shinichi.
Ran gets suspicious of Conan is really Shinichi for the first time.
There are rumors that a mysterious ghost knight is roaming the local art museum, and Ran wants to check it out. When they go to check out the 'Hell' exhibit, they find Manaka, the manager of the museum, has been stabbed to death by the ghost knight. The clues seem to point to one person being the criminal, but Conan isn't convinced.
Conan, Ran, and Kogoro attend a festival when Satoru Imatake, a famous writer, is murdered. Conan is certain that it was Norikazu Sasai, the murdered writer's partner but Sasai has a perfect alibi provided by photographs, including some taken by Ran. Did Sasai really commit murder?
The Detective Boys talk about the Sunday Cup, a soccer tournament, and mention Naoki Uemura and Hideo Akagi of the Tokyo Spirits. Afterwards, Conan returns to the Mouri Detective Agency to find a girl named Ryoko Akagi waiting in front. She asks Kogoro to find Shinichi Kudo, saying that she was his girlfriend. Ran gets jealous and angry and decided to go to her house, but Conan notices some strange things and realizes that Mamoru Akagi, Hideo Akagi's little brother, was kidnapped. After the solution to the case is revealed, Ran calls Shinichi's cell phone, the number of which he gave to Ryoko before, and chases Conan (unknowingly) to an alley where she confronts "Shinichi" about Ryoko. At that moment, Agasa drives up in his yellow beetle and helps Conan out. Conan replies to Ran using the bowtie with words that somewhat suggest feelings for her and he then hides in Agasa's car, escaping from Ran successfully.
Kogoro receives a letter with a large sum of money from Keiji Asoh requesting that he investigate Moonlight Island. On the island, they discover that Keiji was a famous pianist and has been dead for twelve years. They believe the client wanted them to investigate Keiji and so they decide to question the Mayor. They learn that Keiji's piano is in the community hall and that the previous mayor was discovered dead with the song Moonlight Sonata playing in the background and that Moonlight Sonata was the same song Keiji played on his piano during the fire that killed him. During the funeral for the previous mayor, Moonlight Sonata is heard from the piano room and they find another man murdered there. Conan interprets the letter as indicating that the murders are just starting. Conan and the others spend the night near the piano along with Dr. Narumi Asai. The police interrogate everyone the next day who were at the funeral but another man is murdered. Music notes left by the killer reveal that whoever the murderer is is avenging Keiji Asoh.
While playing hide-and-seek in the park, Ayumi hides herself in the trunk of a car and falls asleep. When she wakes, the car has already left the park, and Ayumi finds herself with a head of a girl wrapped in newspapers. Conan uses the radio transmitters the Detective Boys received from Professor Agasa to get clues and find where the car is heading.
A woman named Masami Hirota shows up at the Mouri Detective Agency and asks Kogoro to find her father and only relative, Kenzou Hirota. Rearranging Kenzou's cat's name, they realize it's the name of a racing horse, and find him at a horse track. The next day, Kenzou is found dead and Masami missing. Conan remembers that he accidentally placed a tracker on Masami and tries to track her location but the batteries in his glasses run out. Later, a detective is revealed to be tracking Masami down for his client Akira Hirota who also claimed Kenzou was his only relative.
The Detective Boys watch as a sniper shoots a balloon by the river, but Conan notices that the sniper is held at gunpoint by other men. When the Detective Boys get there, the gunmen are nowhere to be seen, but Conan finds a message on a calculator that the sniper left behind. The message is only decoded when Conan turns the calculator upside down to discover the location of the sniper. The gunmen, holding the sniper and his wife hostage, force him to try and assassinate an important political figure. Can Conan stop the assassination from happening?
While looking for a missing cat, the Detective Boys find the cat covered in blood. Tracing the source, they find a dead corpse in a house. After calling the police, they investigate the house but the corpse is nowhere to be found.
An antique collector, Denjiro Maru, asks Kogoro to investigate his wife's affair, but he is later found murdered. The crime scene is shredded by a sword and fake clues point to different people that had scheduled a meeting with the collector.
The Detective Boys are accidentally locked inside a department store after hours when returning to retrieve Genta's Kamen Yaiba autograph. That night, thieves try to rob the store. They are soon found out and with clever strategies, the Detective Boys are able to apprehend the robbers.
Ran and Shinichi's old homeroom teacher, Sayuri Matsumoto, is getting married, but before the wedding even starts, the bride is poisoned when she drinks her canned juice. Several suspects are caught on video including Sayuri's father, Kiyonaga Matsumoto, and Toshihiko Takasugi, the groom. Who poisoned Sayuri?
Ran is invited to be a model for a fashion designer company. After they arrive, one of the company's employees, Mika Taniguchi, is killed in the elevator. Conan is certain that the company's owner, Eiko Ashiya is the one who killed her but can't prove how as Mika went directly to the 8th floor in the elevator while Eiko went to the 15th.
Ayumi is walking home when she sees lights in an old abandoned house where an unsolved murder took place several years ago. She convinces the Detective Boys to sneak into and explore the house. Genta and Mitsuhiko suddenly disappear leaving Conan and Ayumi following an old woman down a hidden stairs where they find a caged man.
Yoko Okino is starring in a television drama and she invites Kogoro, Ran, and Conan to watch the filming but a cameraman is murdered at the shrine the filming is taking place at! The cameraman left behind a dying message in blood. Can Conan decipher it and reveal who the true killer is?
Kogoro, Ran, and Conan miss their boat home from a vacation and are lucky to hitch a ride with the rich Hatamoto family on a private ship. The head of the Hatamoto family, Gozo is murdered, and the evidence all points to Takeshi whose father committed suicide when his company was taken over by the Hatamoto family. Takeshi is forced into a locked cabin for suspicion of murder. Everyone in the family is interested in the Hatamoto inheritance but are shocked to find that a will was made and the inheritance was signed to Natsue, the Head's granddaughter. Later a Hatamoto family member, Tatsuo, is found dead and Takeshi is missing from the storage room.
Conan finds the crime scene of Gozo strange and believes that Takeshi is being framed. The boat's power is suddenly switched off and Ichiro, a grandson of Gozo, is stabbed in the dark. Everyone is suspicious of one another and accusations are thrown around. After looking in each of the rooms searching for Takeshi, Conan finds the evidence to prove Takeshi's innocence and the culprit guilty.
A woman named Maya has amnesia and stumbles into Kogoro, Ran, and Conan. After leaving the hospital with Maya a car almost hits them and a piece of a building almost falls on them. Conan suspects that someone is trying to kill Maya, but also finds that Maya is acting strangely.
Katsuhiko Takei's daughter, Naoko, is being held hostage by a kidnapper who is demanding 500 million yen. The first transaction meeting fails when the kidnapper finds out Takei called the cops about their meeting and escapes. During the escape, the van drives off the cliff and into the river. Conan finds evidence that the kidnapper escaped, but no evidence of a second person.
Conan is coming back from a restaurant with Ran and Kogoro when they hear a man scream. They enter the house and find a man has been jumped by a dog in the house, causing him to fall backwards off the stairs and into a wall. Pronounced dead, Conan suspects Masayoshi Sakaguchi, the owner of the dog called John. Conan suspects that Masayoshi trained John to kill the man, Takeshi Maehara, who bulled his son, Masato, causing him to suicide several years ago. Conan gives Kogoro subtle hints allowing him to solve the crime.
Kogoro, Ran, and Conan are out walking when a robbery occurs. Conan and Kogoro are able to take down the robber and hand him to the police. A crowd gathered to watch the scene and Kogoro's friend, Yumi recognizes him. After talking about the judo class reunion that is to take place that day, she leaves. While turning back, Conan and Kogoro realize the gun the robber had is missing. That night at the reunion, they plan to go out and watch fireworks. Kogoro's friends did not go leaving only Conan, Kogoro, and Ran. Yumi is missing from dinner so the judo members go to her room to wake her up from her sleep. There, they find her dead from a gunshot wound to the head and in her hand was the missing gun from before. Kogoro realizes that burn marks are missing from Yumi's temple meaning that it was a murder and one of the judo members is the suspect.
Conan recognizes two things strange about Yumi's body; the finger was not on the trigger and she was naked under her robe. Conan then realizes who the murderer is and plans to tranquilize Kogoro to solve the case. Realizing how determined Kogoro is on solving the case, Conan instead decides to drop subtle hints and let Kogoro solve the case.