It seems the notorious Kid the Phantom Thief has returned after eight years. At first, high school student and master illusionist Kaito seeks to challenge the magic trick-wielding outlaw out of pride, but then he learns that his deceased father was actually Kid the Phantom Thief, so who is the newcomer? Kaito puts on his dad's old cape, hat, and monocle and takes to the air to get answers.
Kaito goes up against a Syndicate-owned pool hall hustler to win back the Legendary Cue, a treasure once owned by Jii before he was cheated it out of it by the Syndicate boss many years ago. However, things look dire when Jii's pool hall is put on the line and Kaito apparently has no skill with the game.
A brilliant if arrogant teen detective comes to town, determined to capture Kid the Phantom Thief. This turns the heat up for Kaito, especially since they're classmates. In fact, Kaito becomes Suguru's rival even out of uniform, leading to a "gentlemen's bet" over which of them will go on a date with Aoko.
Kid's first order of business is saving himself and an unconscious, handcuffed Aoko as they plummet from the top of Toto Tower in an antique car. Assuming he succeeds, the next challenge is finishing his mother's last job, bringing a crooked antiques dealer to justice. But his mother never had to deal with the brilliant diminutive detective, Edogawa Conan!
Kaito and Aoko are on a luxury train with the Queen of Ingram, her son, and the Principality of Ingram's Crystal Mother, a huge topaz that may contain the Pandora jewel. The queen has the real jewel cleverly hidden, though, making it a challenge for Kaito/Kid to find it before the train reaches Osaka. On top of that, he's got competition, as there's a Snake on the train!