At the beginning of the movie, Rachel has a flashback of Jimmy taking her to the fountain at Tropical Land.
The movie quickly transitions to Conan calling Rachel in a phone booth. After Rachel asks Conan if he could come back to Tropical Land (thinking he is Jimmy), the Junior Detective League cross his path, making a remark like, "It's not fun if he (Conan) isn't there", Conan quickly hangs up.
It is shown that the Junior Detective League came up with a new riddle that they are confident that Conan cannot solve. However, Conan quickly solves the riddle. When Georder tries to cross the light, a policeman stops him, saying blinking green is the same as a red light. Conan and the rest wait for the next green light, but right when they are about to finish crossing, a mysterious man with an umbrella shoots the policeman in the booth. The man runs, and Conan gives chase, but loses him. When Conan asks the victim if he knew who shot him, the man grabs for his notebook, and fades away.
The Junior Detective League are taken to a police conference because they were witnesses to tell them the details of the man. However, the conference goes nowhere as Amy, Mitch, and George disagree on how the culprit looked. Amy claims the culprit was a middle aged man, Mitcheck claims the culprit was a young man with a black umbrella, and Georder says the culprit was a beautiful woman with a green umbrella. Conan later says that the culprit's raincoat and umbrella were both a shade of gray, and remembers the umbrella was in his/her right hand, showing that the culprit was left-handed.
Later, a woman finds a police officer, Youichiro Shiba murdered in a parking lot, who was holding his police notebook in his right hand. The police, because of the similar conditions, are treating this as a serial killing. When the following morning Richard Moore tries to ask Megure for more details, Megure hangs up, saying that he is busy. Richard notes that Inspector Megure is acting strange.
Megure is later shown talking to Santos, saying that the information between the two cases must remain between them.
Santos's sister later has a party to bless her marriage. When Richard sees Megure again, he tries to get info, but the latter remains shut up. Conan realizes that Megure may know something that is kept confidential. Richard and Conan later try to blackmail Wilder using the info that Wilder likes Miwako. Wilder tells Richard and Conan that the second victim held his notebook during his dying moments. However, Santos leads Wilder away, saying to Richard that this is as far along as he knows, and says, "Need not to know." Conan then deducts the culprit may have been part of the police.
Serena and Rachel are shown asking Eva how Richard proposed to her.
Simone later goes to the bathroom, and Rachel follows her. After that, an explosion occurs, knocking out the lights. The culprit appears and Simone shields Rachel from many bullets. The flashlight shows the culprit's face. Simone is shown unconscious, and Rachel faints when she sees her blood-streaked hands, believing that Simone's injuries were her fault. When Richard asks Megure for Simone's condition, Megure says a bullet stopped close to her heart, leaving a 50/50 chance of her survival. Serena later rushes into the room, saying Rachel has regained consciousness, but is acting weird.
It is shown that Rachel was struck with amnesia, and lost her memory of everybody she knew, including the memories of the current day. However, her brain was functioning normally. After this incident, Megure decides to leak the information about this case.
Megure starts by telling Kogoro of a surgeon named Jinno that was murdered. The leader in the investigation squad was Tomonari; his subordinates were Narasawa, Shiba, and Simone. During the case, Tomonari suffers from a heart attack, but insists that no one worry, and to continue the stake out. Simone follows Tomonari, but he dies from a heart attack. When the remaining two see the targets, they notice that one of them is the Chief's son, Tobias. Back then, the case was abruptly concluded as a suicide. The case reopened when the three subordinates were killed, with the exception of Simone, who was critically injured.
While Richard and Conan are looking over Rachel, Conan comes to the conclusion that she may have witnessed the culprit's face, and mentions that she may be targeted.
Rachel is later discharged from the hospital. When she tries to get out of the car, she seems to cower in fear because of a puddle. Richard reintroduces her to the house, but she seems to notice the picture of Jimmy. Conan and Eva later try to regain her memory.
The next day, the Junior Detective League follow Rachel around as guards. Vi remarks that it may be better if Rachel's memory wouldn't return. Rachel seems to show a strange feeling when she sees Jimmy's picture. That night, she asks Conan about Jimmy.
The following day, Rachel, Eva, and Conan are waiting at the subway station to go shopping. The culprit suddenly strikes and pushes Raches off onto the rails. Conan barely manages to save her life. The doctor mentions that she may be scared to further regain her memory.
Conan later investigates the people related to Jinno, and finally realizes the culprit.
Rachel is later taken to Tropical Land to help regain her memory. She has a flashback of Jimmy pressing the cola against her cheek. Wilder later goes to the bathroom, and a mascot character of Tropical Land suddenly walks towards Rachel. At the moment, Junior Detective League chase the person and take him down. Richard removes the mascot head and it is Makoto Tomonari. He also finds the knife in his chest pocket. Tomonari was about to tell that he's not the murderer but it's too late. Wilder arrests him. The Junior Detective League celebrate their victory. Richard tells Rachel that he's going to the police station for questioning and also tells her to stay at the Tropical Land until she regains her memory.
At the police station, the police are questioning Tomonari. He reveals that he wasn't approaching Rachel but instead he wanted to talk to Richard for his help. He is innocent and the reason why he had the knife in his chest pocket is for his own protection.
In Tropical Land, the actual culprit later attacks Rachel but Agasa tries to protect her and gets shot. Conan hurries and rushes to her aid and quickly takes her deep into Tropical Land, and the culprit gives chase. When the culprit later pins them down to a volcano, Conan reveals his deduction, and also reveals the culprit was the psychiatrist, Kyosuke Kazato, who killed Jinno as revenge for having injured his hands to ruin his promising career, then kept killing to cover his leads—which is why he wanted Rachel dead, as she managed to witness his last murder and see his face clearly despite his efforts.
Conan and Rachel then later escape down an escape hole. They run to a lava lake, where Rachel asks Conan why is he protecting her. Conan replies that he loves Rachel, more than anything in the world...
Conan later takes Rachel to the fountain, the same place where Jimmy took Rachela long time ago, and Kazato finds them and starts shooting at Conan. Rachel then finally breaks free of her amnesia upon seeing Conan in danger and recalling how Simone was shot to protect her; she loudly remarks on all of this and easily disables Kazato, turning him to the police. News later comes that Simone survived the surgery, and will be making a full recovery.
Rachel tells Conan the line her dad told her mom was that he loved her more than anything else in the world, leaving Conan (Jimmy) saying that he can't believe he used the same pick-up line as that stupid old man (Richard).
The film's theme song is "Anata ga Iru kara" by Miho Komatsu (arranged by Daisuke Ikeda).
The VHS of the movie was released April 21, 2001. It was discontinued soon after 2006 as it was switched to DVD.
The DVD of the film was released on January 24, 2001. A new DVD was released on February 25, 2011, significantly lowering the original price and added the trailer as a special feature.
Funimation released the English dub of Captured in Her Eyes on Region 1 DVD on December 29, 2009.
The Blu-ray version of the film was released on May 27, 2011. The Blu-ray contains the same content of the DVD plus a mini-booklet explaining the film and the BD-live function.