The director of the Kurokawa hospital, Daizou Kurokawa was found dead on front of his computer, the words JUN glowing. JUN is the clue, but what? Kogoro incorrectly replies that JUN stands for June, which in turn means waterless month, which in turn means Mina, the wife. Inspector Megure points out that a man on the verge of death would not choose something so hard to figure out to point out the suspect. Conan, tired to waiting for Kogoro to figure out the truth, shoots him with the sleeping needle. Using his voice changing bowtie, Conan solves the crime. The housekeeper, Manami Nakazawa, killed Daizou Kurokawa with blunt object. Before he died, Kurokawa was able to type Mi-na-mi, not before accidentally hitting the English text key. The reason was that one year ago Kurokawa operated on her husband while he was drunk and as a result her husband died. Minami Nakazawa changed her hairstyle and became Kurokawa household's housekeeper for revenge, no one ever noticed.
While at Dr. Agasa's house, Conan finds a letter addressed to him (Shinichi Kudo). It is an invitation to a garden party held by Teiji Moriya, a famouse architect for left-right symmetry. Since Conan couldn't go, he tells Ran to go in his place over the phone using his voice changing necktie. Ran agrees to go under one condition, Shinichi has to go see a movie with her on May 3rd, without his agreement, she continues on and askes him what color he likes better, red or blue. He cooses red, Ran's favorite color. Before Conan could say anything more, Ran hangs up.
What is on May 3rd anyways? May 4th is when Sherlock Holmes and Moliarty fall off a cliff. The next day is Children's Day. Just then Inspector Megure calls Conan's name. Megure introduces Detective Shiratori. Shiratori mentions how Megure told him about Conan's keen eye for things. Conan blushes. Conan goes back to wondering what was on May 3rd.
Back at Ran's place, Conan, Ran, and Kogoro eat dinner, prepared by Ran (looks yummy!). Conan finds out that May 4th is Shinichi's birthday. Ran plans to take Shinichi to an all night movie on the 3rd and when midnight comes around, she's going to present to him a red polo shirt. And the movie they're going to see is "Legend of the Red Thread." The legend is when a man and woman fall in love, a red thread ties them together by the pinky since birth. Kogoro opposes Ran going to an all night romance movie, doing weird things. But Ran adamantly tells her dad that its not that type of movie. Ran then changes the subject to the invitation Shinichi gave her, Kogoro and Conan agree to go with her.
At the Moriya mansion, Ran notices the entire place has left right symmetry. During the party, Moriya give Kogoro a puzzle to solve, and to make it fair for everyone else, he gives everyone the same puzzle question. Conan solves it first as bing Momotaro, the year of birth of the men in the question correspond to the Chinese Zodiac, the monkey, the rabbit, and the bird, Momotaro's companions. Kogoro is obviously unhappy about losing. As a reward, Conan and Ran get to visit Moriya's private gallery. All the buildings in the pictures are symmetrical. As Ran and Moriya talk, Ran mentions that May 4th is Shinichi's birthday and his favorite color is red, like the red thread that ties them together.
The next day, Ran goes shopping for Shinichi's birthday present. At Dr. Agasa's house, Conan and Dr. Agasa watch the news. At a chemicals storehouse, chemical bombs were stolen, but there are no suspects at the moment. In the next news, Kurokawa house hold was set on fire, luckly no one was home at the time. This leads police to believe that the fire was an arson. Because of increase in arson cases and also the similarity, the police believe the arsonist could be the one and the same. Just then the phone rings. The call is for Shinichi. All calls to the Kudo household is sent to Dr. Agasa's house. On the other end of the phone is a man, his voice distored, telling of a bomb in the park. If he doesn't go to the park soon, it'll explode. Then he demands Shinichi to give him his cellular phone number, and Conan reluctantly gives it. Conan then hops on his solar powered skateboard and head for the the park.
At the park are Ayumi, Genta, and Mitsuhiko flying a tiny airplane. Conan arrives and asks them where they got the plane and they reply from a man with a beard and sunglasses. Alarmed, Conan grabs the remote controller and Genta and Mitsuhiko tell him to wait his turn and try to grab it back. Conan blurts out there's a bomb on the plane and the two immediately lets go of the controller, it falls to the ground and breaks. The tiny plane then starts to chase Ayumi, Genta and Mitsuhiko. Conan powers up his shoes and kicks the broken remote controller toward the plane, it connects and immediatly explodes in an orangeish glow, a plastic bomb! Just then Conan's cell phone rings and he picks it up, forgetting to use his voice changing necktie. The bomber realized that the kid is his opponent instead of Shinichi. He tells him of the next bomb is going to explode at 1 o'clock, in about 15 minutes, in front of the Beika Train Station. The hint is that is' underneath the tree, but its not buried underneath the tree. Conan hurrys off the the next location.
Once there, he searches underneath all the tress, but there's no sign of a bomb. Frustrated, he goes to the second floor of a burger restaurant to get a better view of the area. From the window he sees an old woman pull a case from underneath a bench, on the case is "Someone, please take care of this" and inside is a kitten (neko in Japanese). Under the tree's roots (nekko). It's the cat! Conan rushes out to catch up to the old woman, who gets into a taxi cab. Without looking, Conan rushes out into the street and is almost run over by a motorcyclist. His skate board bangs against the curve. There's only 5 minutes before 1 o'clock. Back on his skateboard, Conan slowly catches up to the taxi, but then the engine on his skate board dies. The sky is still sunny, the motor shouldn't have died, unless the solar cells were broken when it hit the concrete. Desperate, Conan borrows a bike from a kid and takes off after then taxi. He is almost run over by the taxi when he catches up to it. Jumping into the taxi, he reaches for the cage and looks inside...and a bomb is patiently ticking away at the bottom!! Taking the case, Conan jumps back onto the bike and speed away, searching for a safe spot to put the bomb. At one point the bomb stops ticking at 16 seconds, but then starts once again. Conan rides off a toward the ravine and jumps off the bike. The bomb explodes in midair, the force of the blast knocking Conan unconscience.
At the hospital, Conan wakes up surrounded by Dr. Agasa, Ayumi, Genta, Mitsuhiko, and Kogoro. Kogoro briefly gets angry at Conan. Inspector Megure and Detective Shiratori come to find out what happened. It seems whoever is doing the bombings has something against Shinichi himself. Megure thinks of a case that might be...
A woman was run over in the rain by either the Mayor Okamoto or his son, Kohei Okamoto, both were in the car, one was driving. The son claims he was the one who was driving, but evidence points otherwise. A used cigarette was found at the sight had the finger prints of the son. Shincihi asks Kohei to sit in the driver's seat and light the cigarette up. Kohei reaches for the cigarette lighter with his left hand..but on the lighter are the fingerprints of his right hand. The only way to light a cigarette from the driver's side is to use the left hand, not the right. This meant that Kohei was in the passenger's side and the father was on the driver's side. Just then Mayor Okamoto confesses to the truth, he was the one who was driving...
But the only way to find the truth is to investigate the son, if he had any hatred for Kudo, they had to find out. Megure then asks Ayumi, Genta, and Mitsuhiko if they remember anything else. They think about it and Ayumi replies that he had a sweet smell, not like perfume... Megure tells them to inform him if the remember anything else. Since there was nothing else for them to do, the three kids decide to go home.
Conan's cell phone rings and Kogoro picks up. The bomber wants Shinichi, but Kogoro replies that he is the bomber's opponent now. Fine, he tells everyone listening that there are five more plastic bombs planted on the the Tokyo train lines. If the trains running right now goes lower than 60 kilometers, the bomb will explode, and they have until sunset to find them. The hint is "xx no x."
The train station office is contated and the operation managers tells them to speed up the trains... The workers are shocked to hear that if the train goes below 60 kilometers/hour, its going to blow up.
On the train, Genta notices that thy're nearing Beika Station but the train is speeding up instead of slowing down. Just then, over the speakers, it is announced that because of an emergency situation the train will pass the Beika Station. The three are surprised...but they didn't know the meaning of "emergency situation..."
At 4 o'clock, Inspector Megure hears over his cell phone that the train didn't blow up. Kogoro exlaims that he figured out what the bomber was talking about. It's either under the seat or overhead, but Megure replies he could also think of underneath the train itself. Agasa asks Conan if Ayumi, Genta, and Mitsuhiko if they would go to the Midoridai Station to rid the Kanjou Line. Conan realizes that they would.
On board the train, the announcer tells the passengers that the train won't be stopping for a while and also if they see a suspicious package not to touch it and immediately notify the conductor.
Conan's voice comes through Ayumi's badge. He asks where the three are. Genta asks what's going on. Mitsuhiko asks if something that starts with a "B" is on the train. Conan assures them that is nothing. Just then Megure's voice comes through telling someone that the bomb could be anywhere on the train. Ayumi asks if they're going to die, Conan replies that's not going to happen, they're going to find the bomb. Genta stands up and tells the others that the's going to find the bomb, and Ayumi and Mitsuhiko join in, too! They cut off the connection with Conan.
Megure and Kogoro goes to the railroad control room where a conterplan headquarters was created.
On the TV, new reporters are flocking at the station and above in the helicopters. In the lobby of the hospital, Conan watches the news. Dr. Agasa brings in a TV from the nurse's lounge to take to Conan's hospital room. Conan wonders why it will explode at sundown, it there a connection with the light?
In a restaurant, Ran and Sonoko chat about her date with Shinichi. Ran comments how her father and Conan are probably wondering what to make for dinner.
At the control room, reports come back about not finding anything suspicious aboard the train.
On board the train, the passengers are getting restless, they demand to be left off. One passenger tried to jump off.
With only 1 hour and a half left, Conan figures out where the bomb is. He immediatly calls Megure (as Shinichi) and tells him that the bomb is between the railroad tracks. The bomb is set to explode after several seconds of shade. The train being a total of 200 meters running at 60 kilometers/hour would take 12 seconds to pass over a small area. If the train slows down to the point where it would take 13 seconds to pass over the same area, the bomb is set to explode. If all the trains transfer onto side tracks, there should be no problem.
Taking Shinichi's advice, the trains are sent to side tracks and slowed down. None of the trains exploded and the passengers were allowed to get off safely. Now it was the police's turn to find the bomb. One by one, reports of bombs came in.
In Conan's hospital room, Inspector Megure tells everyone that the amount of plastic found in the bombs only account for one fourth the amount stolen from the chemical storehouse. That means there will be more bomb threats. Shiratori comes in and tells them that the mayor's son, Kohei was out of near Izu at the time. Kogoro mentions that the bombs planted for the trains aren't near the bomber's house. No one wants bomb parts to come flying near himself. That makes sense because at one point, the second bomb stopped near a playground and a mansion. Conan suggests finding out who was the architect who built the house in the arson case. It might turn out interesting, Conan told Detective Shiratori.
At a subway entrance, Sonoko was going to leave Ran to her date. Ran had one more hour before the movie started.
Back at the hospital, it turns out that Moriya Teiji was the one who build all four of the mansions that had recent arson fires. And they were all build the first half of the 30 years that he was an architect.
They all decide to go to Professor Moriya's mansion.
Over at Professor Moriya's, Conan notices an interesting smell. He sneaks away toward the gallery while Kogoro, Detective Shiratori, and Inspector Megure talk to Professor Moriya. Conan goes through his usual deductions, and begins to piece things together. In the middle of the gallery is a perfectly symmetrical model of a place called, "My Illusiory Mewtown, Nishitamashi." The street lights on the model is the same as the street lights at the park where the bom stopped ticking. Conan finally figured out who the bomber is, but he had no proof. Looking around the room for proof he finds a lighter sitting on the table.
Inspector Megure decides to leave because Professor Moriya couldn't think of anything else that could be of help. Just then Megure receives a call from Kudo Shinichi asking everyone to gather around in the gallery. Moriya picks up the lighter that Conan was looking at earlier along the way to the gallery.
In the gallery, Professor Moriya sees his model uncovered and becomes angry. Kudo calls Megure again, telling everyone that he figured out who the bomber/arsonist is. Kogoro butts in and claims it is Shiratori, ranting out the reasons while Shiratori squirms. Shinichi tells everyone that Kogoro is mistaken, this case isn't about someone with a grudge agains Professor Moriya, it is about the man who tried to burn down four houses, and the one who built that bridge, Professsor Moriya!
Moriy'as archetecture made him famous, but later he wanted destroy all the work he did in his youth. Shinichi tells everyone to look at all the houses that were burned down by arson. All 4 were not perfect in symmetry. The bomb that Conan was carrying stopped where the park was because of the streetlights, a symbol of Newtown, Mishitamashi. Moriya tells Shinichi that he has no proof, but Shinichi replies that he does. He tells everyone to look undeneath the model case, Detective Shiratori finds a pair of sunglasses, wig, and beard. Moriy blurts out that the stuff should be in the safe in his study. Conan comes in and explains that the sunglasses are really his glasses with black waterbased marker smeared on it and the beard and wig are from the decorative hair of the helmet ing the study, and all of this was Shinichi's idea.
Detective SHiratori is about to aske Moriya to the police station when Moriya pulls out the lighter and tells everyone that if they move, he'll expolode the bombs placed in his mansion. Conan tells Moriya that that woun't happen because he took out the batteries. Detective Shiratori then arrests Professor Moriya. Moriya tells them this isn't over yet, there is one more building that he wanted to destroy....the Beika City Building, his worst archetctural product. Only one minute left till 10 PM... Ran...
Conan calls Ran at Beika City Building, but it's too late, the bomb explodes. Building parts fall and people cream in a desperate attempt to get away.
Kogoro gets angry demand what Moriya plans to do. Moriya replies that he only closed off all the entrances and exits to the building, the fun is just about to start. Moriya shouts out loud, "Kudo, I know you're listening from somewhere, if you don't hurry up and go, your precious girlfriend will end up in pieces." Kogoro gets really angry and had to be restrained by Megure and Shiratori. A piece of paper sticks out of Moriya's jacket pocket, Conan sees this and jumps to get it. It turns out to be a map of the bomb. Conan runs off t hand it to Shinichi, Moriya tells Conan to tell Shinichi his message: "For you, I created 3 minutes. Savor it carefully." Megure and Kogoro run after Conan.
At Beika City Building, smoke is rising up, helicopters fly around and people are running away in a frenzy. Firetrucks and paramedics are on the scene putting out the fires and helping people. Kogoro search for Ran in the crowd outside. Conan goes inside the building.
Inside, Ran tries to comfort someone. the phone rings and Ran picks it up. Shinichi is on the other end. Shinichi made it to the emergency door, but because of the blast it is bend out of shape. He asks Ran to search for an attache case or a trunk, or anything unusual. Ran spots a bag behind a seat. Inside is a bomb with about 42 minutes left, it is set to explode at 12:03 AM.
18 minutes left, Shinichi asks Ran if she has a pair of scissors to cut the wires with, Ran moves closer to the emergency exit door. Conan/Shinichi tells her to cute the yellow wire... Somewhere a bomb explodes...
Outside, Kogoro becomes frantic. Moriya, who is still handcuffed, tells Kogoro that there is still 15 minutes left before his daughter is blown away. And that even if they're able to diffuse most of the bomb, the last one will separate their fate.
5 minutes left, Ran continues to cute the wires. Shinichi tells Ran that after the last black wire, the timer should stop. The timer continues to tick after the black wire is cut. There are 2 wires left, a blue and a red wire.
Kogoro tries to rush inside, but Detective Shiratori stops him.
At midnight, a clock rings out, only 3 minuts left. Conan is frustrated over the 2 wires... Ran calls out Shinichi's name, "Happy Birthday, Shinichi...I might never be able to tell you that..." ...Shinichi tells Ran to cut the color that she likes. Whatever happens, he'll be right there. They'll be together when they die.
Just then the building rumbles and concrete falls. Conan had to jump out of the way and on the other side Ran jumps out of the way or falling concrete, carrying the bomb, of course.
Setting the bomb down, Ran thinks of her conversation with Shinichi, dinner with her dad and Conan, her horiscope, and the red shirt she bought. Determined, she lifts up her scissors.
Conan desperately calls Ran's name. Rescue workers come in and try to open the emergency door. One of the workers complain he is not going to be able to slowly savor his wedding anniversary. Conan thinks back and figures out that the red is the trap. Conan tries to run back, screaming to Ran to cute the blue wire, the red it the trap.
32 seconds left... Ran prepares to cut...
Outside, Megure, Shiratori, and Kogoro are quiet. Moriya has a smug look on his face...
"Good bye, Shinichi..."
Ran cuts a wire... everything is silent...
2 seconds...the timer stopped!! Ran cut the blue line. Outside, Moriya is dumbfounded. Inside, everyone is cheering, Ran is relieved.
Everyone is rescued, some are carried away by paramedics. Kogoro is crying ove rthe safty of Ran. The news come and flock around Kogoro...
Ran goes off and searches for Shinichi, but finds Conan instead. Conan asks why Ran didn't cut the red wire. Ran replies that she didn't want to... "Shinichi and I could be tied together by a red thread." Ran smiles and lifts her pinky finger.