Jirokichi immediately opens a press conference, announcing that he will collect all seven paintings scattered around the world, and exhibit them as 'The Sunflowers Admired by Japan' in the Suzuki Financial Group's 'Lake Rock Museum'. Conan and the Detective Boys also attentively watch the conference from the TV in Professor Agasa's house. Jirokichi states he has already contacted the owners around the world, and gained permission for exhibiting them, in exchange for furnishing them with the perfect security, preservation, and transport measures. Jirokichi lauds the specialists he has gathered to fulfill his side of the bargain, the 'Seven Samurai', and invites them on stage. But his laughter is cut short when a card flies through the air and slices into the stage. It was a heist notice with the logo of Kaitou Kid: a Kid Card. Kid then shows himself, pointing his card gun at the crowd, inciting panic and fleeing the scene. But he is pursued by one of the Seven Samurai, Detective Charlie, a security professional. However, when trapped in a corner of the skyscraper, Kid lets off a flash bomb, breaking the window and vanishing into the night sky.
A special plane decorated as the 'Sunflowers Jet' would carry the painting to Japan, along with Jirokichi, Sonoko, the Samurai, and as a special guest, a high-school detective who offered his help in the case: Shinichi Kudo. But just as the jet approaches Haneda Airport, the wall of the cargo hold explodes, the door is blown away, and the painting is carried away into the sky. The engines also end up exploding in the blast, and Sonoko and the others let out desperate screams as the jet goes into freefall. Meanwhile, the 7th Samurai, Kogoro Mori, is waiting with Ran and the others at Haneda Airport for the plane's arrival. But when they spot the plane, it is out of control and having difficulty making a landing. Ran is worried about Sonoko and the others aboard the plane. But then Kid is seen flying through the skies, painting in hand. As emergency vehicles gather around the barely-landed plane, Conan spies Kid. He runs through the airport trying to pursue him, but Kid only sneers and flies away. However, Conan successfully locates the painting Kid had hidden. The Samurai quickly examine it and attest that the painting is fine.
Several days later, Jirokichi invites the Seven Samurai to a conference to plan what counter-measures they can take against Kid. The owners of the other paintings had also become reluctant in loaning him their paintings. That morning, Conan, Agasa, and the Detective Boys head to the Sompo Japan Nipponkoa Museum of Art, to see the 5th painting. Just after Conan leaves, Kogoro receives another notice from Kid. The Samurai decode it and find that the notice states that he will steal the 5th painting tonight. Conan, Haibara, and the others are viewing the 5th painting together with an old woman named Umeno, said to visit and view the painting every day, when Jirokichi, Kogoro, Inspector Nakamori, and the others arrive. Conan quickly realizes a case is unfolding and joins up with them. They decide that they should move the painting to a safe place before night comes, and the painting is to be wrapped up under the instructions of the Seven Samurai. However, Kid had already infiltrated the staff, and steals the painting. He also leaves behind a message to the museum's curator, saying he will return it if paid ten billion yen. Jirokichi immediately decides to pay the enormous ransom. The deal with Kid turns into chaos, however Conan and the others miraculously succeed in retrieving the 5th painting. However, even Conan begins to wonder about Kid's escalating crimes which have come to endanger many lives.
With Kid's motives as yet a mystery, the exhibition of the Seven Sunflowers at Lake Rock Museum meets its opening day. The most excited to see the exhibition are the Detective Boys, Conan, Ran, and Sonoko. Just as they begin to view the paintings, Conan spots a Kid Card. The enigmatic message could not be deciphered by even the Seven Samurai, but its presence attests that Kid is already within the museum. Jirokichi quickly orders to evacuate the museum goers and staff, to trap Kid inside the museum. However, he seems to have anticipates this turn of events, and blows up the electric room, leaving the museum in a blackout. Then, a great fire also breaks out, leaving Jirokichi and the others no option but to send the paintings to their storage room, and evacuate to a special room outside. But, the 2nd and 5th painting could not be collected, and the inferno closes in on them. The only people remaining in Lake Rock Museum are a great detective, a great phantom thief, and...?!
