Kogoro, Ran, and Conan are at a fancy traditional Japanese restaurant where food is delivered on a small computer controlled boat that navigates over a running stream around the restaurant. Later, a murder occurs and Conan realizes the only way it could have been possible was for a person to be alone, and to use the stream to access the room.

Agasa takes the Detective Boys to his uncles house which has been abandoned fifty years ago for a treasure hunt he had set up.

Conan matches the symbols to the Hiragana table and reveals that the symbols in the objects direct to other objects in the room.

The Detective Boys are in a puppeteer camping trip, where they are practicing for a school puppet play. At the same time, a serial killer has been spotted near the areas of the camp. While at the camp, the students disappear with their puppets, leaving the Detective Boys alone.

Hattori Heiji, bringing along Kazuha, is hired by the rich Takeda family to investigate a series of suspicious suicides that has plagued their mansion in Tottori Prefecture.

Conan and Heiji investigate further into the ghastly death of Nobukazu as well as the suicides of Misa, Kinuyo, and Negishi.

Conan tranquilizes Kogoro and cooperates with Heiji to shed light on the case.

Kogoro is invited to an aquarium where an underwater play is to take place, A woman's dead body rises from the water when it's her cue to come out of a clam's shell in the play.

Conan detects a change in Ran’s behavior and speculates that she may have something going on. Kogoro, on the other hand, takes them to his doctor Yoshiteru Araide’s house for a checkup.

Conan establishes that Yoshiteru was murdered and finds several clues missed by the police including a broken piece of a vase.

Ran, Sonoko, and Conan are at the Tropical Land ice rink where they meet a group of people: Yasuharu Misawa, Izumi Sano, Yoriko Komatsu, Chihiro Itami, and Kunitomo Oda. Chihiro goes to the women's bathroom where she is being followed by a cloaked figure.

Bloody marks are discovered at and near the crime scene. Conan puts Kogoro to sleep to reveal that the culprit.

Saizo Kano, known as the Organizer of Shadows, is shot to death by his subordinates, Sadao Kujirai, Korehisa Kanie, and Teruyoshi Kameda. In the present day, while celebrating their last heist on a luxury cruise ship, Kano’s crew is picked off one by one by a mysterious killer. The stakes are raised when Heiji is thrown into the Pacific Ocean while investigating and a bomb is discovered to be hidden on the ship. Is there something more sinister afloat, or has Kano returned from the dead to enact his vengeance 20 years later?

Richard is called to investigate a suspicious murder where three people admit to killing a man for hitting him on the head.

On the way home from school, Conan and Haibara find Gin's Porsche 356 on the street and places a covert listening device in it. Conan hears that a Black Organization member codenamed Pisco is ordered to assassinate someone at a party hosted at Haido Hotel.

Conan investigates and reveals to Haibara that the purple handkerchief will narrow down the suspects.

Haibara climbs to the top of the chimney only to be confronted by Gin and Vodka.

Conan and the group go to a coffee shop. Nearby, two men are having a meeting. One of them gets up to go to the bathroom, and while he's gone, a truck slams into the coffee shop and smashes the other man who was still seated. Conan realizes it was a planned murder and finds evidence through the truck.

Kogoro is invited by Yoshinori Kana to his home to investigate an unknown stalker harassing his wife, Misaki, who leaves mysterious gifts and letters.

The case is solved, the mysterious man was figured out to be a statue hanged by a fishing rod.

The Detective Boys are walking home one day when they discover two s shaped hooks and a ring with the initials M to A, a wedding ring. They decide to investigate seeing it as an S.O.S.

One day, The Detective Boys were bored so they picked up receipts in a convenience store to guess what the people are buying for dinner. George picks up a weird receipt with food items, a dust bin, a container, a handler light, rechargeable batteries, thin lytax gloves, and chlorine.

Kogorou, Ran, and Conan are invited by the hostess of a car accident charity named Shou Beniko. While driving, they find a message from the Phantom of the Cursed Masks who tells them they should not go.

Kogoro is invited to a house as to impress the client's mother who is a finance trader, simply a loaner. Later, loaner is murdered and with the clues, the suspects are her son, daughter, or maid.

Kogoro, Ran, and Conan are driving by when an arrow almost hits Kogoro. Afterwards, they stay at a hotel when an actor is found dead with a bullet in his head and all the evidence suggests it is the work of an outsider.

Conan later solves the case by showing how the culprit tried to place false evidence to lure the police to think it was an outsider.

Ran's strange behavior causes Conan to suspect that she knows his identity as Jimmy. Later on, the Detective Boys are taken by Agasa on a camping trip.

The Detective Boys realize that the riddle is a reference to shogi and that the dragon refers to a promoted rook. They take the direction a rook is placed on the shogi board and escape the cave.

Vi reveals the gun was a fake and reminds Conan the threat that the Black Organization poses.

The police are unable to find the source of the poison from the drinks. As they are able to rule the death as a suicide, the black knight declares it was a murder and reveals his identity.

Shinichi takes Ran to a fancy restaurant in order to confess his love.

After checking the company's mascot, Shinichi confirms Satoru to be the murderer, thus locking the two in a game of cat and mouse.