Conan suddenly wakes up in the darkness. While walking with the Detective Boys to go shopping, Conan witnessed a figure breaking open a safe inside a building. Conan was attacked by the culprit and imprisoned inside a rectangular box. Meanwhile, Kogoro is hired to find the thief who stole the will of Karabashi Group chairman Karabashi Gotaro. The suspects have been narrowed down to Kozo the eldest son, Mitsuyo the eldest daughter, and Hideo the second son. Conan manages to get in touch with the Detective Boys using his badge, but he soons finds himself cornered in a desperate situation...

Conan is attacked by a theif attempting to break into a safe and trapped inside a coffin. Kogoro is hired to find the person who stole Karahashi Gotaro's will and narrows the suspects down to his three children. Conan uses his DB badge to contact Ai and the others and tells them the coffin he's trapped inside is being transported by a hearse. Mitsuhiko hears about the case Kogoro has been hired to investigate from Ran and deduces that it must be related to the robbery Conan witnessed. Ai and the others realize Conan is inside Gotaro's coffin, but the hearse is already on its way to the crematorium...

Detective Chiba is investigating a strange case that took place three months earlier. Magazine editor Kyogo Nakatsu was suffocated to death and pressed face-first into a patch of concrete at Haido High School. The prime suspect is UFO fanatic Yusuke Kuchiki, who testifies that an alien flew down in a UFO and murdered Nakatsu while floating mid-air, and a security camera captured a mysterious shadow.

Conan visits Yusuke Kuchiki's house with Detective Chiba and Kogoro to question him. While there, Conan discovers something in the room and realizes the reason behind Kuchiki's strange actions. Later, Conan confirms the appearance of the UFO. Having closed in on the truth, Conan gathers everyone to conduct an experiment.

When police Officer Yumi Miyamoto sees a news story about the shogi championship match, she learns for the first time that Haneda is a professional shogi player. Several years earlier, Yumi received an envelope from Haneda and was instructed not to open it until he had acquired "all seven." Haneda has now won all seven major shogi titles. Detective Sato reasons that the envelope's contents must be a marriage registration, but Yumi threw out the magazine she kept the envelope in that morning. They immediately head to the dump site, but the magazine is gone. Conan and the Detective Boys attempt to help Yumi find the envelope.

Building manager Koroku Hachitsuka hides the envelope containing a marriage registration form Haneda gave to Yumi and locks his computer with an eight-digit password. The location of the envelope will be revealed when the password is entered. Believing the solution may require more than one sheet of paper, Conan and his friends decide to search the room for the other sheet. During their search, Yumi notices the code sheet is a copy and not the original. This clue leads Conan to the solution.

Kogoro takes Conan and Ran to the Beppu hot springs in Oita Prefecture. Kogoro's true purpose is to find Manami Nakadai, the missing daughter of Nakadai Electric's president. It's highly probable that Manami came to Beppu to see her ex-boyfriend, Hiroyuki Hayami. Kogoro is able to find Manami, but she is then kidnapped. Meanwhile, Detective Miwako Sato and the police are pursuing an armed robber in Oita Prefecture.

Manami is kidnapped, and the bag containing the 100 million yen in ransom money is carried away by Ryuji Ogikubo using a drone. Detectives Sato and Takagi are also pursuing Ogikubo as the suspect in an armed robbery. Ogikubo takes Sato hostage and heads for the hot springs, where he plans to meet up with his accomplice and split the ransom money. The detectives arrest Ogikubo, but the 100 million yen inside the bag has disappeared. Conan pursues Manami and Ogikubo's accomplice in order to solve the case.

While Conan walks with Ran, Sonoko and Sera along a cherry blossom-lined road, Ran recalls how she met Kudo Shinichi. Thirteen years ago, Ran was being bullied by some boys in her kindergarten class. She was approached by Shinichi, who had just joined the school. Shinichi suspects something is up when he notices teacher Ronsuke Efune staring at Ran the whole time. Later, he's suspicious when Efune shows favoritism to Ran. Efune explains each of his actions, but Shinichi suspects Efune is plotting something.

Shinichi tells his parents about Ronsuke Efune's suspicious behavior toward Ran. The next day, Efune takes the children to the park far away from kindergarten. Yusaku Kudo goes to check on the children while dressed in disguise and witnesses the driver of a parked van taking photos of the children. Yusaku learns Efune's wife is staying at the hospital next to the park and begins to unravel Efune's plot.

Conan and Sonoko arrive at a dojo in Osaka where Kyogoku is training. Takami, the master of the dojo, once provided Kyogoku with a great deal of help with his karate training. While Conan and Sonoko watch the children practice, Kajiyoshi shows up to get Takami's signature on their agreement. Operating the dojo has become difficult to the point that Takami has taken out a loan, and he is considering selling the dojo. Later, an important black belt is stolen from the dojo's display case. When Kyogoku is suspected of stealing the belt, he challenges Takami to a fight. If he wins, the dojo will remain open, and if Takami wins, he'll return the belt...

Kogoro and Conan search a fourth-floor apartment when they're asked for help by the trio standing in front of the room: Saki's friend Maiko, building manager Yoshie, and deliveryman Matsuda. Inside they find the bodies of residents Maehara and his wife Saki. Day trader Maehara had recently made a lot of money, and the valuables are missing from the apartment. Inspector Megure deduces from the apartment's condition and the testimony of the trio that Saki pretended to be a robber and murdered Maehara but made a mistake while disguising herself as a victim and suffocated herself. However, Conan notices something strange about the crime scene...

The body of neighborhood nuisance Tatsuya Amagi is found in the park of a high-class neighborhood. He was stabbed numerous times by an awl-like weapon. Next to the body is the bloodstained medical examination card of neighborhood association president Hikoichi Bando. The police head to Bando's home to question him, but discover Bando has been poisoned with a combination of liquor and pesticides, and near his body is a bloodstained awl.

A piece of evidence discovered at Bando's home leads to college professor Yosuke Chino becoming the prime suspect. However, Conan realizes something is off about the case and reasons that the real killer framed Chino. Conan discovers an important clue at a café and realizes what really happened and the identity of the real killer.

While hiking, Conan and his friends meet campers Eiko, Ashizuka, Hayashida, and Takemi at a mountain cottage. The four of them have gathered to commemorate the death of their friend Motoki who accidentally fell to their death three years ago. Takemi, who camped by herself in a tent at the bottom of a cliff, is found murdered the next morning!

Kogoro is hired to catch a thief. While working the case, the body of Junko's neighbor Kitagami is discovered in the parking lot behind her apartment building. Kogoro reasons Kitagami got drunk and accidentally fell from his room, number 704. Conan finds it strange that Kitagami left his front door unlocked when his apartment was fully equipped with anti-theft devices...

Real estate company president Hiyama is murdered while holding a pair of scissors invented by Agasa, so Conan and Okiya accompany Agasa to the crime scene. The man who discovered the body is former candy shop owner Senba. Agasa suspects Senba is the murderer, but it was impossible for Senba to have entered the house with a weapon. The current case closely resembles a 17 year old case in several ways, such as the murder victim holding scissors and the sink left running at the crime scene. Conan and Okiya watch as Senba recreates the steps he took when he discovered the body and notice several contradictions...

Real estate company president Hiyama is murdered while holding a pair of scissors. The crime scene is very similar to that of an unsolved case from 17 years ago. Conan and Okiya believe former candy shop owner Senba who discovered the body is the culprit, but are unable to determine how he brought the weapon inside the annex where the crime took place. Later, Conan and Okiya question the bodyguards standing at the entrance and identify the trick the culprit used to bring the weapon inside. They even find the weapon, and they begin solving the whole case...

Kogoro is invited to go on TV with the Soul Detective who has promised to help solve the mysterious death of Kohji Haneda. When Conan and Kogoro arrive, they find the Soul Detective dead in his room.

Conan and Masumi investigate the Soul Detective murder. While investigating, Conan suspects Masumi is hiding something...or someone in her room. Does this case have anything to do with the murder of Haneda 17 years ago?

An old children's story writer is found dead by her nephew next to the park the Detective Boys are playing soccer at. All three suspects have an alibi, but what does her missing Myna Bird have to do with the case?

While cleaning Shinichi's house, Conan and Subaru overhear Ran and Sonoko talking about a musician about to release lyrics from a song written 17 years ago with the title, ASACA. Something about this leads them to believe it could be related to the Black Organization. When arriving at the musician's rehearsal, Amuro is there with Azusa from the Cafe....but it's Vermouth in disguise!

Musician Hado is found hanging by the neck above the stage of a concert hall. Conan attempts to balance as he does not want his or Subaru's identity to come under suspicion as Amuro begins to bait Subaru into revealing who he truly is. During the case, all three confirm which objects disappeared from the crime scene. Giving a joint deduction, Conan, Amuro and Subaru search the stage and determine the truth behind the case and the trick the killer used to lift the victim's body...

Conan and the others help an old bookseller with books he was unable to carry. While at the store, he's seen arguing with his son over getting new books they don't need. While in the park next door, a stack of books falls over and hurts the owner!

A robbery goes wrong when a gang starts to murder it's victims. One gang member manages to escape, but is shot with a crossbow bolt in the process. While Conan and the Detective Boys are on a weekend adventure with Professor Agasa, they find the shot gang member passed out on a villa property. It seems the gang is still hunting for him.

After falling head first off a cliff into the sea, Conan and the escaped gang member are thought to be dead. Having managed to get into a tunnel under the cliff, they now use their status to try and catch the rest of the gang at their next heist with Haibara's help.

The Detective Boys go to Gifu to explore and see a local hero show. Afterwards, Mitsuhiko goes to ask for their autographs. While waiting, the Detective Boys feel he's been gone a long time. When they go to their tent, they find the heroes and Mitsuhiko have gone missing!

Heiji is invited to Yadori Village along with a historian, archaeologist, reporter, and a writer along with Conan, Ran, and Kazuha. Following a group dinner, a mysterious sound is heard and a fire is started outside. A mythical beast, known as a Nue is thought to be seen outside.

While seeing the Nue outside, the historian goes missing and is found dead in the woods with claw-like marks. Ran and Kazuha move rooms after finding mysterious writings from its deceased inhabitant.

As the Nue appears again, the archaeologist has been poisoned, but everyone was visible while it happened. Conan and Heiji quickly move towards finding the culprit before another murder occurs.

Kogoro, bringing along Ran and Conan, is requested to investigate a Buddha statue rumored to have moved on its own. He meets Eikyo Fukuhara, his family (wife Masako, daughter Yuka, and son Eizen) and Buddhist trainee Junko Wakuda. After dinner, Eikyo displays uncaring behavior, leaves to go pray, and is later found dead with a knife in his neck. Kogoro, after finding clues thanks to Conan, declares Junko to be the killer after he attempted to scare Eikyo. Junko confesses but Conan isn’t satisfied. After finding rice powder near the victim, Kogoro is tranquilized and Conan reveals Masako to be the real killer. She discovered Junko’s scare tactic had failed, stabbed her husband to death, and framed Junko for the murder. Masako confesses stating Eikyo‘s rude and cruel treatment to his family as her motive and has a sense of relief now that he is dead. She maniacally laughs over her actions as she is arrested.

While at a high tech plant, Conan, Ran, and Kogoro witness a murder. One of the employees was strangled. Was it a murder or is there more to it?

A thief makes a run for it after being caught by the person they were stealing from. During his escape, he runs into Genta, who he quickly pushes out of his way. As Genta pursues, the thief runs into another man knocking him unconscious, both tumbling down a hill. When he awakes, he switches clothes to frame the man he knocked out.

As Ran, Sonoko, and Sera try on swim suits, Conan wonders through the department store and overhears a lady accosting the other people near her dressing room. After Conan leaves, he later hears a scream from that area. The rude woman turned up dead.

As Conan investigates the dressing room murder, he thinks about a bigger mystery: what Sera is hiding about her past. Conan and Ran both begin to recall a meeting with her from over 10 years ago.

Conan and the Detective Boys get stranded in the rain and take shelter in a nearby mansion. Upon entering, it is learned the master of the house's wife died several months ago and he believes he is seeing her ghost!

Ten years ago, Masumi, taken by her middle brother Shukichi and their mother Mary, reunite with Shuichi who did not take the test yet to become an FBI agent in the Atsuhama Beach, Shizuoka Prefecture. Mary had an off-screen fight with him where they both managed to injure each other's eye. Throughout the case Mary warns him to stop investigating the disappearance of his father. The Akai family also encountered Shinichi, Ran, and Yukiko who also happened to be there. Shinchi introduces himself as "Holmes Apprentice". All of them end up being involved in a case where two robbers robbed a watch shop with one of them accidentally got killed in an accident, and the other was still on the run.

Ten years ago, immediately after a young Kudo Shinichi meets Akai Shuichi's family on the beach, a car falls off a cliff. It becomes clear the car belonged to two thieves who robbed a watchmaker. The driver died immediately, but their accomplice fled from the sinking car and blended in with the crowd on the beach. With the help of Shinichi and his friends, Shuichi narrows down the suspects to Fukumizu Shigekatsu, Kitamori Yasue, and Oami Raiya. The police detective decides to question the three of them, and Shuichi determines which of them is the robber based on their testimony...

A pop-up book and pink smartphone arrive at the Mori Detective Agency. The book turns out to be a warning of the serial bombings that have been occurring. The culprit is Hirukawa Takuji, half-brother of Imai Kenichi, the now deceased author of the book, and a man with a previous bomb manufacturing conviction. Due to his hatred of detectives, Hirukawa chose the famous Kogoro to become involved in the case. The locations of the bombs are riddles, and Conan works with Kogoro, Megure, and publisher Tomonaga Hiroyuki to find them, but...

A pop-up book and pink smartphone are delivered to the Mori Detective Agency. In the pop-up book are warnings of a series of explosions. The riddle for the location of the third bomb is "the middle of 7." Conan and his friends think of things expressed in sevens and what the middle of those things might be. In a week, it's Thursday. In a rainbow, it's green. In a musical scale, it's fa. Overwhelmed by the number of possibilities, Kogoro holds his head in his hands. At the police station, they begin searching for places, companies, and schools corresponding to Thursday, Green, and fa, but Conan reasons that Hirukawa's target lies elsewhere...

Conan and Heiji go to Poirot to while waiting for Ran and Kazuha. While there, a gathering of old friends is quickly interrupted by a power outage. During the blackout, one of them turns up stabbed with blood splattered everywhere. Yet, nobody has blood on them...

With all of the possible suspects having no blood on them, Conan and Heiji quickly discover the method used. Now they need to discover the motive.