The game begins when the president of a successful banking company, Kouzou Yamakawa, is found dead in the office of his mansion. Kouzou's body is reported to the police by his secretary Fumie Sawaki, who discovered the corpse when she had Kouzou's elderly gardener break down the office door after finding it locked. The autopsy report concludes that Kouzou died at 9:00PM on the 17th of June. The police investigation discovers that the office was locked from the inside, which suggests that Yamakawa committed suicide, but the player is dispatched from the Hyogo prefecture police department to investigate further.
Aiding the player is Yasuhiko Mano, an assistant investigator who speaks on behalf of the silent protagonist and does the legwork for the case. Insisting on being called Yasu, he informs Boss that the residents of Kobe have not seen a man named Hirata since the night of the murder. Investigating the Yamakawa mansion leads to the player discovering a ring on the doorstep and a matchbox hidden under an ashtray in the room where Kouzou perished, along with a photograph. Examining the mansion's living room yields a discarded lighter under the table, which all combine to set up several red-herring endings for the investigation. The player also has the option to question Fumie, but Yasu becomes considerably defensive around her and prevents harsh interrogation.
Questioning the locals at Kobe harbor tells the player that the troublesome nephew of Kouzou, Toshiyuki, was witnessed at the harbor on the night of the murder after 9:00PM. Investigating Toshiyuki's apartment when he is not home exposes his connections to drug trafficking, and when called into the questioning room he will confess to his crimes after Yasu engages in police brutality. Arresting Toshiyuki but being no closer to solving the case, the duo bring in Kamiya for questioning, Kouzou's gardener who discovered his corpse along with Fumie. Kamiya admits that on the night of the murder he snuck out for alcohol and foolishly left the front door to the mansion unlocked. Calling in Toshiyuki for further questioning and showing him the collected evidence, the drug dealer points out that the ring was a bauble he gave to a highschool girl he was sweet on named Yukiko.
When Yukiko is called in for questioning, her alibi is that she stayed home on the night of the murder. A neighbor witnessed her leave the house. She visited the mansion at 7:00PM June 17th to ask Kouzou to lend her father, Hirata, more money to pay off his older debts, stating that he borrowed money from other lenders that were vicious in their collection practices and that she hoped Kouzou would be more lenient. Asking for her father's whereabouts, she informs the police that he was last seen at Amitabha Peak in Kyoto. There, Boss and Yasu discover that Hirata has committed suicide by hanging himself in the forest. Yasu then concludes that Hirata was the murderer and killed himself out of shame, but the autopsy report lists his death as 1:00PM June 17th, thus proving this is in fact the first red-herring ending.
With the case growing well beyond the initial assumptions, Boss and Yasu perform gumshoe work by questioning the citizens of Kobe once more. Questioning a bartender reveals that Kouzou had a serious fight with a man named Kawamura sometime prior to the events of the game, flying in the face of the kindly old lender persona the man had cultivated in the city. Boss and Yasu are later led to a strip club where one of the women reveals much about Kouzou's past. The stripper, Okoi, explains that Kouzou had a very shady past with Kawamura: the two were con-men who would stoop to any low to extort their mark. Okoi would also explain that Kawamura kept Kouzou on a tight leash by threatening to expose his past crimes should he disobey him, leading to their brawl in the bar.
Okoi will later call the police to notify them that Kawamura has been seen at the Sumire apartments. There, Boss and Yasu discover the corpse of Kawamura laying on the apartment floor. Yasu attempts to close the case by concluding that Kawamura murdered Kouzou and took his own life after realizing there was no where to run to, but this is the game's second red-herring ending.
Left without further leads, Okoi is called into questioning once more and reveals that Kawamura offhandedly told her of the biggest score he and Kouzou pulled off in their criminal careers. Their largest victim was a company called Sawaki Industries, located in Sumoto on Awajishima island, which was driven into bankruptcy by their actions. Okoi then remembers that the last name of Kouzou's secretary was also Sawaki, but she is running late for her show and cannot stay to ponder. Travelling to Sumoto and questioning the residents about Fumie reveals her tragic past: her parents committed suicide when her father's company was victimised by con artists and driven to bankruptcy, and she was sent away to live with her relatives. Fumie was also separated from her older brother, a man with a birthmark shaped like a butterfly.
Returning to the police station, Boss and Yasu are informed that officers discovered a map of the Yamakawa mansion in Kawamura's apartment, revealing the underground maze beneath the mansion. Returning to the scene of the crime and examining the painting in the living room activates the trap door leading to the maze from Kouzou's office. Descending into the labyrinth, Boss and Yasu navigate through the corridors and discover Kouzou's secret journal behind a false wall. Reading it reveals that Kouzou regretted his life of crime and felt strong remorse for driving Fumie's parents to suicide, deliberately hiring her as his personal secretary as a way to try and make amends. The journal further states that Kouzou planned to watch over Fumie as if she were his own daughter and leave considerable money to her as part of his will; this information leaves Yasu notably shaken up.
Back at the police station, the player has the option to order Yasu to remove his shirt: on his shoulder is a birthmark shaped like a butterfly. Yasuhiko confesses his crimes, stating he killed Kouzou and Kawamura to avenge his parents. On the night he killed Kouzou he used a key he found in the mansion to lock the door to the office behind him, but when notified that the police discovered the key to the office on the inside, Fumie enters the questioning room to confess her part in the cover up. Yasuhiko had given her the key after committing the murder and leaving the scene of the crime, and when she asked Komiya to break down the door the next morning she slipped the key into the lock while the older man was still in shock from seeing Kouzou's corpse.
Yasuhiko takes a moment to reflect on the irony the he only learned of Kouzo's remorse for ruining the siblings' lives after murdering the old man. Overwrought with complicated emotions, brother and sister cry out one another's names as the game ends.
