The culprit is Satoru Andou. Satoru Andou did it because his wife was killed in the fire Etsuto Murobashi is responsible for setting it up so he can steals a valuable picture in the mansion unnoticed.
While the deduction show still continues, Scar Akai enters the room belonging to the mysterious lady and throws her luggage out the window. The mysterious woman appears at the door and tells Scar Akai that the dress in the luggage was her favorite. The mysterious woman reveals herself to be Yukiko Kudo by naming Scar Akai as her old friend, "Sharon". Scar Akai rips his mask off and confirms Yukiko's deduction that he is none other than Vermouth.
Yukiko boasts to Vermouth that they got a hold of Vermouth's weak points, which is Vermouth that doesn't want anyone, including her partner on the train, to know that Conan and Haibara shrunk from the APTX 4869. Also, Vermouth had ordered software from CG programmer, Suguru Itakura that probably is related to the de-aging. Yukiko also showed her surprise that Vermouth had a fight with Itakura on the film set even though Sharon is known for her consideration for the staff. Vermouth responds to Yukiko's boast by saying she is the one who saw through Yukiko's team's plan. Vermouth deducts that they will try to fake Shiho Miyano's death so the Black Organization will let go of her for good. Vermouth explains then that Haibara can't be shown dead in her child body because it will cause the Detective Boys to panic and cry, which would bring the Black Organization's attention to them as Sherry's acquaintances. But if Haibara dies in her original body (played by Yukiko with makeup) and those who know her secret keep quiet about that, then the Detective Boys will be none the wiser. This scene will also result in heavily checking the passengers' belongings upon disembarkment and the Black Organization won't be able to take "Sherry's" body away to confirm her identity. Vermouth tells Yukiko that's not only Yukiko's luggage that she disposed of, but the bullet-proof vest with blood contraption that she hid in the basin closet as well. Yukiko say the two are even because even Vermouth sees though her plan but hasn't found Haibara. Vermouth reveals her trick to smoke Haibara out by detonating mutilple smoke bombs she placed earlier. (The bombs can be seen under the attendent's seat and also in the crime scene.)
At the deduction scene, Amuro is the first to notice the smoke, concludes the train is on fire and tells everyone to evacuate to the front of the train. The suspects, who are pyrophobics after surviving the mansion fire incident, become panicked and run. But Conan has to wake up Kogoro and urges Komino and Sumitomo of room D to hurry up and leave. Next, Vermouth correctly deduces that Haibara won't escape the fire to the front like everyone else, but will go in the opposite direction. Then Haibara is shown, now in her original body, running through the smoke past the victim's room (7B). A voice from behind states that Shiho is "as expected of Hell's Angel's daughter" that she is "very much alike". The voice belongs to Amuro, who introduces himself to Shiho with his codename, Bourbon.
Ran meets Kogoro and asks him where Haibara and Sera are (she assumes he'd know because they should pass his deduction site at some point), but Kogoro doesn't know. The train conductor tries to calm the passengers down from panic about the fire and tells them that the staff has yet to know the full details on the situation but will try to find out as soon as possible.
Meanwhile, Vermouth continues to predict Sherry's movement that she will head to the back of train and be killed by the Organization in a silent fashion, rather than involving her friends. Conan then phones Yukiko to inform her that he can't find Haibara anywhere. Vermouth grabs Yukiko's phone away and impersonates her on the phone, telling Conan that Haibara probably escaped to the front like everyone else. Vermouth then receives a message from Bourbon confirming that Sherry is indeed in carriage 8. She then boasts to Yukiko that's it's her team that has the advantage.
In carriage 8, Bourbon tells Sherry he has met her parents and sister. Sherry says she has heard about him and knows he is a rival to Moroboshi Dai, Akemi's lover. Bourbon says Dai was an FBI mole, as he suspected. When he heard that Dai/Akai was dead, he didn't believe it at first and enlists Vermouth's help to disguise himself as Akai, hanging around people who knew Akai to observe their reactions. However, this time he had Vermouth disguise as Akai in place of him. He comes to the conclusion that Akai is really dead.
At the Nagoya train station, Gin comments that the presence of the Jirokichi and Aichi police only make the explosion seem like an attempt on their lives, which covers the Black Orgainzation's intention. He then becomes surprised when Vodka informs him Vermouth was asking for more explosives for the plan, without telling him the purpose.
Bourbon, meanwhile, reveals his plan to take Sherry back to the Black Organization alive. He'll have her step inside the storage hold, knock her out, bomb the carriage link to seperate the storage hold form the rest of the train, then have a helicopter on his side take her away. Sherry refuses cooperate, stating that the storage hold is full of explosives, causing Bourbon to realize that Vermouth had altered the plan, wanting to kill Sherry from the start. Sherry steps away behind the door, while a mysterious figure appears behind Bourbon, obscured by smoke. Bourbon asks if the figure is Vermouth; the mysterious figure throws a hand grenade at him. Bourbon, surprised at this, asks who the person is. The figure is revealed to the readers (but not to Bourbon) that he has Shuichi Akai's face, without the scar, and dresses in an outfit like those of Okiya Subaru's, wearing Sera's hat. The grenade explodes, interruping their one-sided conversation. The storage hold is seperated from the train, and seconds later, it explodes, triggered by Vermouth's cellphone.
Vermouth explains to Yukiko she purposefully detonated the second bomb having heard the first one (which confirmed that the storage hold was separated from the train), making sure the explosion wouldn't cause the train to derail. Vermouth leaves the room while Yukiko begins frantically calling for Haibara, but she stops immediately after Vermouth is out of sight. Bourbon is left wondering who the figure was, but he seems to have an idea.
The train stops and the passengers disembark. Vermouth phones Gin about the situation, in which Bourbon claims he saw Sherry die in the explosion; Gin shows doubt about Sherry's survival. Gin points out that Vermouth wanted an explosion on the train so the train couldn't reach its destination at Nagoya (where Gin was waiting). Vermouth tells him they have to be questioned, along with other passengers and that he should be satisfied enough hearing that Sherry is dead. Vermouth hangs up and overhears the Detective Boys talk to Agasa (who has Haibara sleeping on his back) about how they found Haibara in room 7B. What happened was that Haibara got dizzy after taking the drug for her cold and decided to rest there. The room was empty due to it being a crime scene. Vermouth realizes Yukiko's team figured that Haibara would go there, so they waited for her there. Conan's phone call to Yukiko was just an act to keep Vermouth in Yukiko's room while they took Haibara to saftey. But Vermouth can't figure out who the woman who was supposedly killed in front of Bourbon is.
Vermouth then figured out Kaitou Kid's involvement after overhearing Sonoko voice her frustration to Ran that Kaitou Kid won't be able to board the train after the explosion. Vermouth also overheard Conan on the phone with Kaitou Kid, apologizing to him for draging him into a situation with guns and bombs. Kaitou Kid is shown leaving the exploding train on his hang-glider, the gadget Conan deduced Kid would hide in the storage room in the first place. It is revealed in a flashback that Conan had deduced Kid's identity. He disguised as Hiroka Sumitomo (the maid) and had his accomplice disguised as Natsue Komino (The wheelchair lady). His accomplice, heavily hinted to be Konosuke Jii, can't mimic the voice of the lady, and relies on Kid to voice both of them. He just mouths the words (similar to when Conan solves case as Agasa). So when Conan has Sumitomo run in the corridor, Komino can't speak. Conan has the advantage of being short (looking from below) and saw through Jii's act easily, as well as their reaction about the fire, which wouldn't match the reaction of a pyrophobic.
Conan brings up the point that he purposefully overlooked Kid's actions to avoid being involved with the case as leverage to ask Kid for help. Conan shows him a video of Shiho Miyano and has Kid disguise as her. Conan tells him to be careful because guns and explosives are involved. Conan finishes his conversation by asking Kid to return his cellphone to the detective agency. Kid, annoyed, comments that Conan should be in debt to him for helping, rather than the other way around.
Because of the explosion, the train is brought to an early stop and the passengers disembark so they can be questioned by the police at the station. Konosuke Jii, Kaitou Kid's assistant, has removed his old woman disguise because he is unable to speak without Kid to assist him. Sera tries to figure out what's going on as Ran return her hat which she found in the corridor. Bourbon watches them silently and then asks Vermouth to give him the files from before and after Akai's death one more time. Vermouth agrees and Bourbon thinks he must reopen his investigation from "square one". Lastly, Subaru Okiya, watching Vermouth and Bourbon from behind, opens one of his eyes for the first time to reveal his Shuichi Akai-like eyes.
Scar Akai meets with Masumi on board, and her reaction verifies the Organization's theories of Akai being "dead." Scar Akai has Masumi tasered and put back in her cabin. Yukiko confronts Vermouth, who was posing as Scar Akai for Bourbon to move about, and Yukiko states Haibara will live despite the syndicate's attempts, as Conan has planned ahead for this encounter. Bourbon confronts Sherry wanting to bring her in alive, but a mass of smoke blocks his view as she enters the next cart he was planning to take her in. Vermouth reveals to have planted enough C-4 to destroy the train-car as she was expected to kill Sherry this time. After Sherry "dies" in a fiery explosion, Vermouth exits the train as a tourist and sees Haibara with her friends, realizing she lost the battle. Sherry was really Kaito Kid who was planning to use the train for his next heist, but Conan knew it was him disguised as one of the suspects and said nothing as Conan needed Kid to fake Sherry's death. Bourbon meets up with Vermouth and decides to review the case files on Akai's death after being stopped by an unknown figure. Okiya Subaru, on the train assisting Yukiko, shows his eyes that of Shuichi Akai.
