High school detective Shinichi Kudo goes with his friend, Ran Mori, too an amusement park and solves a murder that occurs on a roller coaster. Shortly after, he tails two men in black and discovers them perform an illegal trade. Kudo is then attacked by them and was forced fed a poison and left to die. A rare side-effect of the poison, however, transforms Kudo's body into that of a child instead of killing him. Adopting the pseudonym Conan Edogawa, Kudo hides his identity to investigate the two men in black and stays with Ran and her incompetent private investigator father, Kogoro Mori. Kogoro is hired to investigate the kidnapping of a president's daughter. Conan locates her using one of the family dogs and saves her. Pop Idol Yoko Okino is suspected of murder when her stalker is found with a knife in his back. Conan knocks Kogoro unconscious and uses his voice-changing bowtie to solve the case while posing as Kogoro, revealing it to be suicide.

Il detective liceale Shinichi Kudo si reca con la sua amica, Ran Mori, in un parco divertimenti e risolve un omicidio che si verifica su un ottovolante. Poco dopo, il ragazzo nota due uomini sospetti vestiti di nero che sembra stiano facendo qualcosa di illegale. Shinichi chiede quindi a Ran di tornare a casa e li segue: non si accorge però che uno dei malviventi è alle sue spalle. Il ragazzo viene colpito e costretto ad assumere un veleno, l'APTX4869. Un effetto collaterale di questa sostanza però, trasforma il corpo di Shinichi in quello di un bambino. Adottando lo pseudonimo di Conan Edogawa, Shinichi nasconde la sua identità per poter continuare le indagini sugli uomini in nero. Il bambino resta a vivere con Ran e con il padre della ragazza, l'incapace investigatore privato Kogoro Mori. Kogoro viene assunto per indagare sul rapimento della figlia del presidente di una società. Conan utilizza uno dei cani di famiglia per individuarla e la salva. La Pop Idol Yoko Okino è sospettata di omicidio, dopo che il suo stalker viene ritrovato con un coltello nella schiena. Conan anestetizza Kogoro, utilizza il suo papillon cambia-voce per risolvere il caso e rivela che l'uomo si è suicidato.

Conan is enrolled in to Teitan Elementary and after class, notices Kogoro shadowing a man in an overcoat. Kogoro reveals he was hired to follow the man for three days and is paid handsomely at the end. On the fourth day, the man is dead, with Kogoro certain his employer is the murderer but has a solid alibi. Conan discovers the employer was posing as the man in the overcoat on the third day, as the man was already killed. After leaving evidence, the police apprehend the employer. Kogoro is hired by a young woman to search for her father. They find him and the next day, discover him dead and his daughter missing. Conan's investigation leads him to discover that the two were involved in a bank robbery for the two men in black. Conan's school friends, Ayumi Yoshida, Genta Kojima, and Mitsuhiko Tsuburaya, ask him to accompany them as they explore a haunted house where a murder occurred five years prior. As they explore the house, Conan discovers the victim was murdered by his son and the supposed haunting was the son and his mother hiding from the authorities. Conan convinces them to turn themselves in and they comply.

Conan inzia a frequentare la scuola elementare Teitan. Dopo le lezioni, nota Kogoro che si aggira in zona con fare circospetto. Il detective rivela di essere stato ingaggiato per seguire un uomo per tre giorni e che verrà pagato profumatamente alla fine. Il quarto giorno, l'uomo muore e Kogoro è certo che il suo datore di lavoro sia l'assassino, ma questi ha un alibi solido. Conan scopre che il terzo giorno il datore di lavoro si era sostituito alla persona pedinata, mentre l'uomo era già stato ucciso. Viste le prove presentate, la polizia arresta il datore di lavoro. Kogoro viene assunto da una giovane donna alla ricerca di suo padre. Kogoro e Conan riescono a trovare l'uomo ma il giorno dopo, scoprono che è morto e la figlia è scomparsa. Le indagini portano Conan a scoprire che i due erano coinvolti in una rapina in banca per i due uomini in nero. Ayumi Yoshida, Genta Kojima, e Mitsuhiko Tsuburaya chiedono a Conan di accompagnarli ad esplorare una casa infestata nella quale cinque anni prima era stato commesso un omicidio. Mentre esplorano la casa, Conan scopre che l'omicidio è stato commesso dal figlio della vittima e che la madre lo ha rinchiuso per impedirgli di essere catturato. Conan convince i due a consegnarsi alla polizia.

Conan, Ran, and Kogoro are given a ride on the Hatamoto family cruise ship after missing their return boat. During their cruise, the head of the Hatamoto family is murdered and the fiancé to the victim's grand-daughter is the prime suspect. The fiancé's father killed himself when the Hatamoto family tookover their company and is cited as the murder motive. Conan's investigates and uses his tranquilizer watch and voice-changing bowtie to impersonate Kogoro. He declares the fiancé's innocence and declares the grand-daughter's cousin as the murderer, citing unrequited love as the motive. Kogoro is hired by a surgeon who has been receiving monthly toys and money to identify the sender. Conan investigates while at the same time, Ran suspects him to actually be Shinichi. Conan identifies the sender to be the father of one of the surgeon's patient who died during surgery and who plans to murder the surgeon's son. After stopping the murder, Conan has Hiroshi Agasa call Ran using Shinichi's voice, tricking him from Conan's true identity.

Conan, Kogoro, and Ran go to a museum where the owner is murdered by a suit of armor. Conan determines the museum director is the murderer and has Kogoro expose it. On the train, Conan runs into the two men in black who refer to each other as Gin and Vodka. He overhears that they planted a bomb on the train. After the two depart off the train, Conan tracks down the bomb before it detonates and removes it from the train. Conan and his friends find a paper coded with symbols after mistakenly switching bags with a man. Conan realizes the message refers to neon lights and follows the code where they find a treasure of gold coins. An Italian gang who stole the gold coins attempts to steal back their goods but is apprehended by Conan. Afterwards, Ayumi becomes infatuated with Conan and kisses him on the cheek.

Ran's friend, Sonoko Suzuki, invites her to attend a film club's reunion party at a villa. Conan and Ran meet a mysterious man covered in bandages on their way. The bandaged man starts to kill members of the film club one by one as the night goes on. Conan tranquilizes Sonoko and impersonates her to expose the murderer, the fat member of the film club who was only pretending to be obese. Ran is invited by Sonoko to meet the members of a band at a karaoke parlor. The lead singer dies after singing his favorite song. Conan solves the case by using the bow-tie set to his original voice and reveals the manager to be the murderer. Afterwards, Ran waits outside of Shinichi's house waiting for him. Conan manages to give her a Christmas present while posing as Shinichi and manages to keep his identity a secret. Later, a woman posing as Conan's mother kidnaps him after revealing she knows his true identity. Conan escapes and begins investigating on her and her companion, a mysterious masked man.

Conan discovers the woman and masked man to be his actual parents, Yusaku Kudo and Yukiko Kudo, who were told of his situation by Agasa. They offer to take him to America with them but Conan refuses as he wants to be with Ran. Kogoro is hired to investigate the affair of the wife of an antique collector. The collector is murdered and his last three visitors are the suspects. Conan tranquilizes Kogoro and reveals the visitor experienced in Iaidō is the murderer. Later, Conan and his friends form a detective group called The Junior Detective League. They take on a request to find a lost cat. They find the cat had invaded a home where they discover a man drowned in his bathtub. When the police arrive, the dead man answers the door and the crime scene has been cleaned. Conan reveals the man is the murderer and had been impersonating his twin brother who he killed. Conan, Kogoro, and Ran attend a festival when they become involved with a man who is a prime suspect to murdering his roommate. Conan suspects the man to be the murderer but has an alibi supported with pictures.

Conan tranquilizes Kogoro and reveals the photos that prove the murderer's alibi were taken from last year evidenced by the tan lines. The next day, Kogoro receives a letter requesting him to investigate something at Tsukikage Island. When asking the residents of the island about the identity of the sender, they discover the name matches a famous pianist who died many years prior. A string of murder relating to the deceased pianist begins and Conan begins to investigate. He determines the killer to be the doctor who is the son of the deceased pianist. The doctor stays in a burning building and kills himself, matching the way his father died. A girl visits the Mori agency requesting them to search for her boyfriend Shinichi. Conan tells her Shinichi will meet her at her house if she takes Ran and Conan with her. As he investigates, Conan realizes the girl wants Shinichi to investigate a kidnapping case involving the brother of star soccer player for Tokyo. The kidnapper demands the girl to tell her boyfriend to forfeit his match or lose. Conan realizes the kidnapper is the teammate of the star player and proceeds to locate him.

They rescue the kidnapped boy and Ran's misunderstanding of Shinichi's relationship with the girl is fixed. Agasa enters Kogoro into a contest where the winner receives a fully paid night at a luxury hotel and a floppy of a famous virus called the Night Baron. The winner must correctly find who is the Night Baron out of the seven participants. After one of the participants is dropped from the hotel and onto a statue, Conan investigates the identity of the murderer. After doing so, he tranquilizes Kogoro revealing the university student's girlfriend as the murderer. Later, Ran, Sonoko, and Conan attend their music teacher's wedding. She is soon poisoned and the groom revealed to be the culprit. Conan reveals that years later, after the husband's misunderstanding is cleared up, the wedding was successfully resumed.

Conan is playing hide and seek with his friends when Ayumi falls asleep in a trunk of a car where she finds a severed head. Conan uses the Junior Detective League badge to find her and chases the car with his solar powered skateboard. They discover the drivers were actors and the head to be a prop to a play. Since they damaged the prop and knocked out one of the actors, they are forced to substitute the missing parts. Kogoro has a class reunion with his Judo club. When the manager of the club is murdered, Conan investigates and drops hints allowing Kogoro to solve it. Kogoro points out his former club captain as the murderer and subdues him with a Judo throw. Later, Kogoro is invited by the rich company owner's daughter as an entertainment for her guests. She reveals that she will pick a man from her party to become her husband. Soon after, the cars of the guests have been slashed leaving them stranded at the mansion. The guests are soon murdered and Conan and Kogoro begin investigating.

Conan tranquilizes Kogoro and reveals the murderer's identity to be the suitor with the glasses citing the water stains on his shirt. High-school detective Harley Hartwell arrives in Tokyo to search for Shinichi in order to test his deduction abilities. Harley accompanies Kogoro as he investigates the murder of a diplomat. Harley reveals his deductions but is corrected by Shinichi, who has returned to his normal form after drinking the Chinese alcohol Paikaru. After correcting Harley's deductions, Shinichi reverts back to Conan without revealing his identity. Conan plans to drink more of the alcohol to become Shinichi again, and opts to play with the Junior Detective League one final time. At the library, they overhear one of the staff is missing and stay overnight to investigate. They discover the library director had been smuggling drugs through the books and murdered the staff when he was found out. After apprehending the director, Conan returns home and drinks the alcohol only to find it ineffective. Conan wins a ski trip and is accompanied by Kogoro and Ran. When they lose their keys, they are invited to stay at a university professor's chalet. The professor is fatally stabbed but leaves a message for Kogoro to decipher before dying.