Conan, Ran, and Sonoko meet up with Eisuke who is looking for his long lost sister. His sister looks identical to the famous newscaster Rena Mizunashi, but Eisuke claims they are not the same person. They head to a fan of Rena to make sure, but when Ran tries to contact him, a mysterious man continues to answer the phone claiming she dialed the wrong number. They head to his mother's house as a last resort where they discover the fan is on vacation and the mother might be victim of remittance fraud.

After watching a video concerning Rena and Eisuke, Conan contemplates if the two could really be related after learning they have different blood types. He informs Jodie of what he learned, and considers that the Black Organization could be using Eisuke without him realizing it. Elsewhere, Shuichi Akai watches over Kir in the hospital which reminds him of a similar accident involving him and Shiho's older sister Akemi. The next day, Conan and the gang pay a visit to a mansion where Eisuke's deceased mother used to work to retrieve her effects, while Kogoro is introduced to an unsolved murder case.

The mansion owner, Kakuzo Okudaira, explains to Kogoro the person who murdered his son a year ago might be someone living in his household and the murderer might return to kill him next. Conan, Kogoro, and the rest of the group is introduced to Kakuzo's wife, Eiko, and then shown to the living room. The group rushes to Kakuzo's room after a power outage and a loud crash. Kakuzo screams to not come in the room, but the butler and maid disobey to find Kakuzo hanged and his 50 million yen vase broken. The police determine Kakuzo was murdered and attempt to analyze a blood covered book that could be Kakuzo's dying message.

Kakuzo Okudaira's wife, butler, and maid are interrogated about their actions prior to Kakuzo's murder. Eisuke discovers the photo of his mother missing and returns to the pool where he slipped and fell earlier to search for it. He finds it at the bottom of the empty pool and when he climbs back up, Conan realizes something that helps him solve the case. Back at the crime scene, Kogoro still believes Kakuzo committed suicide. Conan stuns Kogoro to use him to reveal the trick behind the murder and explain that Kakuzo's dying message points to Kikuyo the maid who also murdered Kakuzo's son the year before using a similar trick. Kikuyo confesses and explains she murdered them because they murdered their former butler.

Eisuke has been missing since the winter break after he found a clue of the whereabouts of a member of his father's company. Coincidentally, the member is at Haido Central Hospital, where Rena Mizunashi is secretly held at. Conan meets with Jodie who confirms Eisuke has been seen at the hospital and reveals that Eisuke's father was a secret CIA agent who died four years ago by the hands of Rena. Conan follows Jodie to the hospital to search for Eisuke and begins to believe Eisuke might be in trouble because the member of his father's company is really a member of the black organization. Conan talks to a nurse to discover there's a patient in the hospital who is also looking for Rena.

The FBI use Conan to question three suspicious patients so the actual member of the organization won't suspect their involvement. After recording his questioning, they use what they've learned to determine who the fake patient gaining info on Rena Mizunashi is. Question is, will they be able to stop him from making his next move?

Rikumichi Kusuda, the fake patient who the FBI is spying on, sneaks into the nurse's office and takes pictures of the list patients. He is caught by a nurse and the FBI deploy. Rikumichi unravels the bandages around his neck to reveal he has C-4 explosives and makes a getaway in a car. Akai follows him with Conan who was hiding in the back, but the chase is cut short when Rikumichi shoots himself. Conan broke Rikumichi's cell phone prior to the escape, but it's too late, the Black Organization already knows where Rena lies. Back in Rena's room, Eisuke walks in demanding her to wake up and tell him where his sister is. Just as Eisuke is about to stab her with scissors, Rena grabs his hand.

Jodie and James of the FBI plan to transfer Rena to another hospital using three transport vans. Meanwhile, all at once, there is a food poisoning outbreak, a gas leak, and a fire which causes traffic and chaos around the hospital. Also, James receives Aquilegia flowers from the deceased Black Organization agent, Rikumichi Kusuda, which contains a small time bomb. Jodie and another FBI agent named Camel rush to detonate it in a remote location. To make matters worse, James is not the only one who received a ticking present from Rikumichi, but every patient in the entire hospital.

Rena appears on television while the FBI agents are gathering the small explosives. The confusion cause the agents to run back to Rena's room, but it's a trap because the explosives the agents were collecting also have transmitters allowing the Black Organization to know where Rena is specifically located. This forces the FBI to transport Rena immediately in the three vans. Chianti, Korn, Vodka, and later Vermouth follow the vans to determine which van Rena is in. Although clues reveal Rena to be in the second van which Shuichi is following in his Chevrolet, Gin forces his team to follow the third van that Camel is driving.

Rena wakes up and knocks out FBI agent Camel, which stops the chase. Once freed, she reunites with the other members. Chianti prepares to kill Camel, but the vehicle explodes. Onlookers appear, causing the BO gang to flee. Later, Andre is alive and Jodie and James learns that the Akai and Conan intended to unite Rena Mizunashi with the other members all along, and explain their plan. It's revealed that Rena is a CIA agent who was undercover as a BO member. She was forced to kill her father after she made a mistake that would've revealed her secret.

Professor Agasa takes the kids to a hotel for food. Later, a murder occurs, and Takagi and Inspector Megure appear with three suspects. Chiba shows up a few minutes later pulling another suspect by the arm. To Conan's surprise, it turns out turns out to be no other than FBI agent Andre Camel, who is the number one suspect due to the fact that he's all sweaty from running. Camel claims he was excercising. Can Conan help clear his name?

The Detective Boys attempt to solve the mystery of the murder, and gather info on their suspects. Jodie arrives on the scene to help clear FBI Andre Camel from suspicion. Also, a note is discovered in English that says "Bring my Tux". What does this message have to do with the murder? Elsewhere, Gin has a private talk with Kir and gives her a way to prove herself to the organization, but the cosequences are deadly. Will she be able to pull off the mission successfully?

Shuichi agrees to meet Kir. James Black is against the decision, but Shuichi explains that he has to, fearing the worse for Kir if he doesn't. Elsewhere, Jodie and Conan have figured out who the culprit behind the murder is. They use a trick involving the Japanese phrase "Shiranpuri" on the suspects. The result reveals the true murderer who doesn't react at all to the phrase, unlike the others. Later, Ran has a bad feeling involving Akai.

Shuichi goes to meet up with Kir. It turns out to be a trap. As told, Kir follows Gin's instructions and eliminates their only threat to the Black Organization. The FBI is eventually informed, and Takagi confirms the death. The news hits Jodie the hardest who has flashbacks of her partner. While driving by her motorcycle, Vermouth notices a distraught Jodie and says to herself that only one Silver-bullet is needed, not two. Later, Jodie returns a fake cell phone in place of Conan's real cell phone who notices the switch, but does not say anything.

Eri goes to a hairdresser to get her hair done. Conan and the others come across a dead body outside. Conan finds the woman who did Eri's hair to be the killer, but with Eri as her alibi, it makes it difficult to prove she did it. What was the trick used in order to carry out the crime?

The woman who does Eri's hair is the killer. Kogoro gets a phone call from his friend to go gambling instead of taking Eri to dinner.

Sonoko, Ran, and Conan once again meet up with Eisuke. They go to a karaoke spot. On their way there, they are followed by a man with hat and sunglasses. Later, this same man turns up dead at the spot, and Conan finds Eisuke to very suspicious. Is it possible he had something to do with the murder?

Conan knocks Sonoko out with a tranquilizer and solves the case. Afterwards, Eisuke reveals he wants to ask Shinichi Kudo for permission to admit his love to Ran and take her to America. Conan tells him he can not and Eisuke confesses that he had found out at the very beginning that Conan is indeed Shinichi.

A child asks the Detective Boys for help on investigating someone who is doing something weird. They are told to come by tomorrow. The next the kid's apartment has been burned down. The only clue to the culprit is the kids Diary, mentioning the Yellow guy who argued with the kid's father. Now Conan must solve this mystery while Sherry senses a black organization member nearby

Conan solves the case and allows the person Sherry suspects to be a black organization member to stay at Shinichi's House. There is a rain of paper planes which people have labelled a prank. Afterwards Conan finds out the planes have morose code with the words S.O.S. Ran with Sonoko tagging along, is on her monthly cleaning trip to Shinichi's house and finds Okiya Sabura. They show the plane to Okiya and he tells them it's an S.O.S

Sonoko decides to have a contest between Shinichi and Okiya. Conan at school solves the paper plane and texts the results to Ran while Sonoko listens to Subaru Okiya's deductions. They both deliver the results at the same time and find the Kidnapped person who is sending the S.O.S.

Mouri is invited by a horoscope reader to meet for the publisher. She is later found dead in her room. Conan figures out the culprit by figuring out his simple plan.

Moore is invited to have his own show. On the way to meeting the manager, he is found dead in his House with the chain lock on. With no way the culprit would've escaped, Conan wonders if this is an impossible crime.

Moore and the policemen have deducted the wrong conclusion that this room is not a locked case and that the criminal told the victim to lock the door and the victim died of poisoning. Conan proves them wrong stating how the coffee spill is weird and how the cake is cut in two but put together in one plate. Conan shows them it is indeed a locked room case and that the murderer is not with them. The case is solved with a sad conclusion, in the rainy day.

Sonoko's Uncle sets up another trap to catch Kaito Kid. This time he holds the Purple nail as the treasure for KID. KID swoops down and takes it and the Uncle sets up a nets on the side so KID is trapped. KID however appears twenty second later on the roof of a building and escapes, declaring he shall return again the next day for the second pair of the purple nail. The next day, Kid uses his trick again to appear on the roof of a building but is intercepted by Conan. Conan reveals that by using sand bags and one of the reporters tied to a rope, he was able to leverage himself to the top of the building.

Conan, Kogorou, and Ran are investigating a strange string of murders and cross paths with Heiji and Kazuha, who are also investigating the same crimes. They learn that the murders are linked to Takeda Shingen and his chosen war strategy Fuurinkazan.

After the four deaths linking to Fuurinkazan are complete, the families return to their homes and await the police's final checks. Conan, Heiji, and Officer Yamato ambush the murderer before they are able to kill the final target.

While out on a trip for their homework assignment, Conan and the Junior Detective league rescue a young girl being assaulted. She later comes to the detective agency to speak with Kogorou. They decide to investigate after learning that a treasure is involved. During their travel to Tsuwano, the young girl meets with her friend, who seems suspicious. While investigating, the girl, Haibara, and Mitsuhiko are abducted.

Conan investigates further and learns where the treasure is. As they reach the spot where the treasure is hidden, Conan puts Kogoro to sleep and reveals the truth behind all the suspicions. He reveals the treasure was the will to change a country, not buy it. Afterwards, Conan revealed there was a stamp on the letter that revealed the treasure worth millions and was supposed to be used to change the country, but was ripped up in the culprit's rage.

Kogoro is invited to a wine appreciation party by Shiratori. While there, Conan witnesses an argument between two men and sees one attack the other. When he finally arrives at the crime scene, there is no sign of the attacked man. The other man is obviously hiding him, but Conan cannot seem to find proof. After finding a reason to trick people into entering the cellar, they find the victim unconscious and the culprit is arrested.

Kudo Shinichi receives mail from a village of a case he solved a year ago. Conan, Mouri, Ran, along with Heiji and Kazuha decide to visit the village and realize that the village hates Shinichi for his deduction of a double suicide relating to the head of the village. Conan heads to the cottage where the letter mentions but turns out to be a plot to trap him there. Later, Conan realizes the cold medicine he took was actually the prototype antidote to the APTX 4869 and that he will become Kudo Shinichi again. Later, Kudo Shinichi is found in the lake with no memory. Afterwards he is found at a murder scene of a news reporter who was going to reveal a secret of Shinichi. Apparently, the murder is related to the mysterious person in the forest, the Shiragami.

Ran wakes up in a hut in the woods and discovers someone has treated the wounds from when she fell. Eventually, Kazuha finds Ran and calls Kogoro in. Heiji radios them from the next room. They all go over and find that the room is filled with pictures of Shin'ichi with knife marks in them. Heiji figures out the case, and they head back to Hinohara's house. There, Heiji reveals that Shin'ichi is actually Makoto, who used plastic surgery to look like Kudou Shin'ichi. Shirigami-sama steps into the room and is revealed to be Shin'ichi. After Makoto is arrested, Ran, Heiji, Shin'ichi, Kazuha, and Kogoro walk back toward the hotel. Before they can reach it, APTX 4869 starts to wear off, and Heiji helps Shin'ichi escape to the bathroom to change back. Haibara had been hiding there, and she gave Shin'ichi another antidote. Then, she says to return to Tokyo before he changes back if he wishes to keep his identity a secret.

While investigating, they narrowed down the suspects to three drivers. After solving the case, the antidote to the APTX 4869 begins to wear off. Ran holds onto his hand, wanting to hear his answer to her question, saying she will never let him go.