Conan and Ran are visiting Heiji and Kazuha in Osaka when the four come across a trio of kids while touring the city. These children, who look eerily similar to the Detective Boys but with different personalities, are looking for their friend who has gone missing—and the two young detectives agree to help find the vanished boy.

Mitsuhiko Tsuburaya lends Conan Edogawa a massive amount of manga, which Conan starts reading, despite the overwhelming quantity. Elsewhere, Kogorou Mouri is asked by the Mine family to protect the treasured sword in their dojo, as Kaitou Kid has sent a note of his intent to steal it. Upon arriving at the dojo, Conan and the others meet Yaiba Kurogane. Together, they aim to thwart the phantom thief's plans. However, Conan begins to notice something strange about the case...

Conan Edogawa and his classmates are assigned to do a class report about a small business of their choice. After discarding other possible topics, the Detective Boys concludes that it's a perfect opportunity to find out more about Detective Kogorou Mouri's job. Conan's friends refuse to settle for a simple interview though, as they want to experience first-hand all the details of his work. Thus, they, along with a reluctant Conan and Ai Haibara, decide to tail the renowned detective for a day. However, the kids soon get involved in a grim situation when Kogorou's current case takes an unexpected and dangerous turn.

Professor Agasa asks Conan for a special favour: to come over to the Beika baseball park, where Ai and Agasa are already waiting. Here, Minae a baseball-playing young girl tries to compete in an otherwise all-boys team, but has a hard time of it. According to the coach she only seems to be lacking a bit of self-confidence. On her way back to the bench she stumbles over a baseball bat that the legendary player Matsui Hideki rammed into the ground. Supposedly any player who swings this bat gains the strength of a real baseball player, and with it any ball can be hit. Time for Conan to take fate into his own hands... for Minae's sake.

One day Mori Kogoro's private detective agency receives a blackmail call. It turns out that the caller has dialed the wrong number. Conan is able to identify the voice on the phone, it's similar to that of his old friend Heiji, who's also a high school detective but in Osaka. They join once again forces to solve the case and find the jewel which was stolen. But they are not the only ones who are after the jewel. The notorious master thief Kaitou Kid has taken an interest in this piece, which is worth 100,000,000 Yen, as well and now it's up to Heiji and Conan to be the first to find the culprit and acquire the jewel.

Sonoko is writing a script for a play. In her script, there's a murder case, and high-school detective Suzuki Sonoko is there to help solve it. Haibara finds flaws in the deduction section of the plot, and Ran decides to call Shinichi for help with the script.

This OVA takes place ten years in the future and chronicles the possible events if Conan Edogawa and Ai Haibara do not take the antidote to APTX 4869 and grow up alongside their friends Genta, Mitsuhiko, and Ayumi, while still maintaining their detective endeavors.

Once again, Kaitou Kid has a target in mind: the Crystal Mother, Europe's largest topaz owned by Queen Selizabeth of the Principality of Ingram. He intends to steal this jewel while the Queen is stuck on a train from Tokyo to Osaka. However, Kid's abilities are put to the test, as the Queen has already concealed the gem somewhere aboard the train. Conan Edogawa, who is among train's passengers, suspects an attack from the phantom thief and begins investigating on his own, while Inspector Ginzou Nakamori is ready for a new confrontation against the elusive jewelry robber.

Conan Edogawa and the rest of the gang are invited to Inspector Ninzaburou Shiratori's villa for a small gathering. The party's highlight is Shiratori's prized wine collection—including his most expensive vintage—and a bottle from it will be served for the evening. However, just as this wine is to be brought out, Shiratori finds the bottle smashed on the floor—and the culprit can only be among the 16 people present in the gathering.

Diana invites Kogorou and Ran to London, but since Conan cannot travel with his invented name, Ai gives him a temporary antidote, letting him travel as Kudou Shin'ichi. Together with Professor Agasa they are on a plane to London. Back in Japan, Ai now lives with Ayumi. Near their apartment, a suspicious man clothed in black named Kurokawa Youji has been trying to track down and now has found Ai. Shortly after Mitsuhiko notices a picture in a magazine of a foreign actress named Grace Aihara, who looks exactly like Ai, Conan calls, ominously instructing Mitsuhiko to keep Ai away from the Professor's house. And so, Mitsuhiko and Genta go about trying to protect Ai...

In this entirely new story produced specifically for the DVD, Conan leads a group of young detectives against the phantom thief Kaitou Kid, who has his eyes set on a jewel at a hotel on an isolated island.

Professor Agasa is kidnapped and the Detective Boys must use clues found at his house and in various parts of the city in order to find him.