The Girl from the Black Organization and the University Professor Murder Case
 Characters introduced
 Case 1: Missing Older Brother Case
A new girl named Ai Haibara transfers into Conan's class. Conan is apathetic, but the rest of the Detective Boys are excited. She acts rather cold and reserved when the Detective Boys try to befriend her, and Genta notices she's looking at Conan suspiciously. She tells them she lives at Beika 2-chōme, 22-banchi, which Conan deduces is right near his house, but can't think of any candidate houses or apartments where a Haibara family has lived.
After school, the detective boys check Genta's locker where their detective group cases are received and Genta finds a request in his shoe. Ayumi tells Haibara to come along with them. The request is from a first grade boy named Toshiya asking the Detective Boys to find his high school aged brother who has been missing for a week. The Detective Boys, along with Toshiya and Haibara, investigate Toshiya's older brother's room. Conan notices the older brother's wallet is still in his drawer which rules out running away from home, and he also discounts kidnapping for extortion because kidnappers would have gone after Toshiya instead. The Detective Boys find the older brother's artwork which are copies of famous paintings. The fidelity is good, but not good enough to be used as forgeries. Conan takes interest in a portrait of Natsume Sōseki which had been in a city exhibition. Toshiya reveals that, before his brother disappeared, a woman in a hat wearing black had an interest in that portrait and approached Toshiya's older brother. Conan panics, thinking that this could be the work of Black Organization. Haibara observes Conan's sudden attitude change.
The Detective Boys search around town to ask whether anyone has seen the woman or Toshiya's brother without luck. The detective boys stop at a convenience story for drinks and Conan notices that a man wearing a black jacket and hat used a ¥1000 bill to pay for ¥330 cigarettes. Conan thinks that the transaction probably wasn't for change because the man could have also bought the same cigarettes at a vending machine outside faster. Conan grabs the bill from the startled cashier and notices it has no watermark; it's a counterfeit ¥1000.
Conan and the detective boys start following the man in black. The portrait on ¥1000 bills is Natsume Sōseki, so Conan explains that the man's counterfeit may have to do with Toshiya's brother's disappearance. In a fit of oblivious deductive monologue, Conan starts talking about the men in black shrinking his body in front of the detective boys. Conan cuts himself off quickly and says it was a joke, but Haibara took notice anyway. Conan decides to plant a tracker on the man in black. Conan tells the man he dropped a ten dollar bill which the he snatches from Conan without realizing a button transmitter was stuck to the bill. To keep them from danger, Conan ditches the detective boys by telling them he has something to do and they should look for Toshiya's brother tomorrow. Ai watches as Conan runs away...
Now alone, Conan tracks the bill to a vender where the man in black bought a ¥110 can of iced coffee. A janitor testifies that the man used a ¥500 coin to buy a train ticket which left him with at least 3 coins of change. Looking at the ticket prices, Conan deduces the man went to Daitoma station. Once there, Conan begins to question a local broker who may have rented a space big enough to print fake money. The broker then asks Conan if he is with the kids outside; the detective boys, Toshiya, and Haibara have been following Conan. Haibara was the one who predicted Conan might try to continue investigating alone and suggested they follow. Toshiya then describes a quick phone call his missing brother made; he said something about being with people like Sōseki. The broker tells the kids he rented a location by the local police post to a newspaper printing company 2 years ago and they recently hired a new worker. The broker says the lady in charge favors wide brimmed hats. With this, Conan realizes the meaning of the hint that Toshiya's older brother said over the phone.
 Case 2: Murdered Professor Case
Haibara reveals that she accidentally sent a floppy disk containing data on the Black Organization to her older sister... which is now in the possession of her sister's professor, Masami Hirota.
Agasa takes Conan and Haibara there to retrieve the disk, only to realize that Hirota has been murdered. The suspects are Hirota's three students who visited that day.
 Episode Resolution
 Manga to anime changes
- In the anime, Haibara tells Conan she escaped from the Organization via a laundry chute; in the manga, it is referred to as a trash chute (ダストシュート).
The names of the APTX 4869 victims on Haibara's list are:
- ?? 宗男 (Status: Dead)
- Surname not visible
- Possible given names: Muneo, Norio
- ?石 良雄 (Status: Dead)
- Surname not visible. (?-shi used by Viz)
- Possible given names: Yoshio, Ryouyuu, Nagao
- 工藤 新一 (Status: Uncertain)
- Surname: Kudo
- Given name: Shinichi
- 豐田 稔 (status partially visible, probably "dead")
- Possible surname: Toyoda
- Possible given names: Minoru, Toshi, Minori, Jin, Jinji, Nen, Yutaka
- 羽田 浩司 (status not visible)
- 野本 昌治 (status not visible)
The anime adds a few extra names, with furigana. In the anime, the names are ??? Kojima, Muneo Arimune, Yoshio Ōishi, Shinichi Kudo, Minoru Toyoda, Kōji Hada, Masahiro Nomoto, Masahito Yoshioka, and Konzō ???.