Queen Sakura, sovereign of the European kingdom of Vespania, is killed while the royal court (her brother and son) are out hunting. All indications suggest that she was accidentally shot by her son, Prince Gill, who immediately commits suicide, overcome by guilt. This news is reported around the world, with a reminder to the audience that Vespania was already recently in the news, because of the strange new minerals found only there.
With the death of the queen and prince, the young but bratty Princess Mira is next in line. However, there is a popular movement in Vespania that says the princess is too young and unfit to govern. Duke Keith, the chief of Commons, hires Daisuke Jigen as the princess' personal bodyguard. Jigen had recently been hired recently to train the nation's military, and the guards allow him to see the Queen's Crown, which is protected by a formidable array of sensors.
To increase the princess' popularity, a trip around Japan is organized. A festival is held at the Grand Hotel West City Tama. Despite her protests, Mira attends the opening, though Keith does all the talking for her. Kogoro Mouri, Sonoko Suzuki, and Conan Edogawa attend (Ran Mouri is running late). At the party, Conan exposes an attempt to assassinate the princess via poisoned wine (the sommelier smelled of cigarettes—not only would this be a huge social faux pas, smoking is a huge taboo for wine-tasters since tobacco would dull their senses of smell and taste). The princess wants nothing more than to escape from her condition, so in the confusion that follows, she sneaks away. Conan notices this, and follows her. Mira runs into Ran, who looks identical. They trade places, Ran returning to the hotel. Mira gets picked up by Fujiko. Conan notices the two splitting up, and Conan pursues Fujiko on skateboard.
After a nice Chase Scene, Conan is shaken off, and returns to the hotel where Ran agrees to go on pretending to be Mira. She does it partly because she wants to experience more of being a princess, partly for avoiding a diplomatic incident, and also because Duke Keith wants a double in case someone is targeting the princess. Meanwhile, Fujiko takes Mira out for a night on the town.
Meanwhile, hidden beneath the kingdom is a mineral that thanks to its "complete stealth powers" may be totally invisible to radar. Using dowsing rods, Lupin has located the mineral. Lupin and Jigen escape with a piece of ore that has incredible stealth properties, though it would have been easier if Jigen hadn't trained the Vespania military to be so effective.
Using a fake press conference at the airport, Duke Keith breaks his promise to return Ran, and brings her to Vespania. Conan, who noticed what Duke Keith was doing, sneaks aboard the jet. Kogoro is given permission to chase after them, acting as assistant to Zenigata, who is traveling to Vespania to stop Lupin from stealing the Queen's crown. Conan triggers an alarm in the landing gear compartment so people find him before he dies of hypothermia at high altitude. This impresses Duke Keith enough that he teams Conan with Jigen to protect the princess, who he thinks is in danger from her uncle, Duke Girald. Ran learns that Mira has only started acting up since her mother and brother were killed. Lupin and Fujiko bring Mira to the cherry blossom tree where her mother and brother died, to give her a chance to grieve. Mira decides to return to take her place as queen.
The princess Mira has since been reported to be back in Vespania. Lupin learns how the princess's character was transformed into a cynical and selfish one due to her unhappiness with her status as princess and her grief due to the death of her mother and brother. It turns out that Fujiko was hired by Duke Keith to remove the princess from court life to make her feel, at least for a while, the typical teenage experience. After meeting with Ran and Kogoro, Conan begins to investigate the murder of the Queen...
Lupin takes Fujiko back to the palace to collect her payment for taking care of Mira, giving her a break from being a princess and a chance to be a regular teenager. Lupin runs into Jigen, and Ran is reunited with Conan and Kogoro. Lupin takes the opportunity to steal the crown, only the discover Fujiko has stolen his stealth device and the crown before him. However, the police arrive before Fujiko can get away. Goemon is needed to carve a way out out of the vault for Lupin.
Zenigata collects everyone in the palace. Conan shoots Kogoro with the tranquilizer, but it misses and hits Zenigata instead. Conan tries to fix the situation by using his voice modulator as Zenigata, but he snaps out of it too quickly. However, Kogoro is actually Lupin in disguise. Our protagonists work together to reveal that the queen had swapped the bullets from the prince's ammo with blanks, so the only one who could have shot the queen was Girald. Girald wants to mine the stealth ore, but Queen Sakura refused because it would pollute. Girald tries to escape, but his trap is neutralized and his guards disarmed.
Mira becomes queen, and Lupin relates the time he met her mother, the last time he tried to steal the crown. Lupin and his gang help sneak Conan back into Japan. Conan vows, if they ever meet again, that he'll arrest them all.
