Conan and Haibara's encounter with the Black Organization at Haido City Hotel

While walking home from school one day Conan and Haibara come across a black Porsche 356A parked  on the side of the rode. Haibara reveals that it's Gin's car. Conan and Haibara breaks in and places a homing device and a bug, so they follow behind and listen in doc's car.

Conan hears Gin talking to Pisco about a murder, then Gin finds the homing device and wire tap, along with one of Haibara's hairs, so he assumes she put the devices in the car.

Conan makes his way to Haido City Hotel where the assassination is supposed to take place. He intends to stop it, and to also get the APTX 4869 which he believes Pisco may have on him.

The it is revealed though a phone call Gin makes that he will also make his way to the hotel with the intention of killing Sherry. Also, he refers to APTX 4869 as "Prototype detective". This is because in Japanese 4869 can be read as "shi ya ro ku" which is similar to "Sherlock". And, before settling on "Sherlock Holmes" Conan Doyle's original name for him was "Shelling Ford", in other words the "prototype detective".

At the hotel a politician is murdered. Among the suspects are Masuyama Kenzo (Pisco) and American Actress Chris Vineyard. During a panic in the crowd, Haibara and Conan get separated and Haibara is abducted by Pisco and locked in a wine cellar in a wing of the hotel that's under construction.

Fearing death, Haibara tells Conan that Apotoxin(APTX) 4869 stands for "Apoptosis" or "Programmed cell death". Each cell has a "sell-destruct" mechanism. Cells receive a signal that restrains it. But, the drug induces the cell to commit suicide, and triggers increased Telomerase activity (a process involved with the protection of DNA and RNA during reproduction). Haibara attempts to download the data on APTX 4869 from a computer left in the room by Pisco, but Haibara had drank Baigar in order to revert to her normal size and escape through the chimney and she started to change. Also, that's right when Gin and Vodka showed up, finding her location with a tracking device in the laptop Haibara was using.

Haibara makes her way to the rooftop but is confronted by Gin and Vodka. Gin shoots her in the arms and leg but just as he's about to kill her Conan shoots Gin with a sleeping dart and tells Haibara to run, using his voice changing bow tie. Haibara escapes back down the chimney, as Gin shoots his arm to stop the tranquilizer dart.

Haibara falls back down in front of Pisco, but she and Conan escape through a fire that Conan starts. Pisco is then killed by Gin. Gin says it's an order from their "boss". Gin escapes through the chimney.

Pisco wasn't caught by the police because the police were looking for someone missing a handkerchief related to the murder at the hotel, but after Chris Vineyard was questioned she gave Pisco her's. She was called there to provide back up for Pisco. Chris Vineyard is called "Vermouth" while sitting in the back of Gin's car, and she says she will be staying in Japan in order to clear a few things up.