Eight years after the mysterious death of his father, Kaito Kuroba, a slightly mischievous but otherwise ordinary teenager, discovers a shocking secret: the Phantom Thief Kaito Kid—also known as "The Magician Under the Moonlight"—was none other than his own father. The former thief was murdered by a criminal organization seeking a mythical stone called the Pandora Gem, said to shed a tear with the passing of the Valley Comet that comes every ten thousand years. When the tear is consumed, the gem supposedly grants immortality. Vowing to bring those responsible for his father's death to justice, Kaito dons the Phantom Thief's disguise, stealing priceless jewels night after night to find the Pandora Gem before his enemies can use the power for themselves.
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 finds himself double-booked when a theft he announced beforehand is on the same night as Aoko's birthday party. Complicating matters is the appearance of a group of jewel-collecting thugs who may have had something to do with the murder of Kaito's father.
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.
Kaito has a new classmate, Akako, who appears to possess genuine magic abilities, the kind that bend everyone to her will... except for Kaito and his alter ego, Kid the Phantom Thief! Who will come out on top in the inevitable showdown, sorceress or illusionist?
Kid the Phantom Thief attempts a bold clock tower robbery in a building swarming with the police, but his real rival takes the stage here for the first time, turning the endeavor into a fierce battle of wits!
When Inspector Nakamori catches a glimpse of Kaito's face during an attempted robbery, the young magician has to "prove" he's not Kid the Phantom Thief by going on a date with Aoko at the same time Kid is supposed to make his next appearance!
Real magic comes back to haunt Kaito in the form of Akako. This time, the sorceress is so annoyed with her classmate that she plots to wipe him out when he's in his Phantom Thief identity. And to stack the deck, Akako turns Inspector Nakamori into a murderous thug!
In the present, Kaito and Aoko are lured into a trap at the top of the Toto Tower, while in the past, the first Kid the Phantom Thief and the mysterious Phantom Lady have an exciting first encounter at the top of the Eiffel Tower!
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!
The Detective Conan crossover concludes with a night at the museum, in which Kid goes out of his way to return stolen items amid a crowd of adoring fans, the police who want to take him down, and a couple of real criminals!
When the greedy owner of a department store has an employee impersonate Kid the Phantom Thief to steal the Star of the Giants, he doesn't count on the real Kid showing up on Christmas Eve to foil his plan!
Kaito takes a break from thieving to go on his class ski trip, but when his teacher holds a couples-only masquerade ski tournament, he finds himself in a tug-of-war between the witchy Akako and childhood friend Aoko!
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!
When a princess with a priceless jewel comes to town, Inspector Nakamori is sidelined by a detective from her country who shoots first and... shoots again later, until his quarry is killed. Naturally, his target is Kid the Phantom Thief!
Kid the Phantom Thief literally rises to the occasion when old man Jirokichi of the Suzuki conglomerate throws down the gauntlet. But with Detective Conan as part of the security team guarding the Blue Wonder jewel, will Kaito finally get his wings clipped?
Kid's next target is Green Dream, the world's largest emerald and a one-time-only stage prop for a local play. Though the venue is crawling with cops under Nakamori's command, will Kid be able to make off with Green Dream as well as make a young actress's dream come true?
Kid has a new phantom thief rival in town, who flew all the way from France: Chat Noir! The felonious feline challenges Kid to steal a cat's-eye ring which may have belonged to Marie Antoinette, but this time, tough security measures have also been imported from France.
Right on schedule, Kid the Phantom Thief makes his move to steal Marie Antoinette's cat's-eye ring off the hand of Inspector Nakamori... but has the French cat burglar Chat Noir already made the first move? And will either one of them be able to escape the "inescapable cage"?
Kid is pressured into teaming up with Nightmare, a masked criminal mastermind with a penchant for losing partners to police custody and sometimes death itself! Will Kid make a successful steal and survive the night?
Kid the Phantom Thief accepts another challenge from old man Suzuki, which means Conan will be on the scene, too. Although given short notice, Kaito tries to think of a show-stopper of a trick to impress his rival and get away with the jewels.
Kid's next target is Red Tear, a gem that belongs to the leader of a magic troupe. But just as he changes his mind after realizing something important, Kaito notices that Snake and his henchmen are also after Red Tear. What's a phantom thief to do?
Corbeau the Phantom Thief, a black-clad, dead-ringer for Kid's father, appears and challenges him. Kaito agrees, but if he fails, he'll have to retire as a phantom thief!
In this final episode, Kid goes up against the enigmatic Corbeau one more time as they vie for the jewel that may contain Pandora, which means Snake can't be far behind!