File No. 009: Good Cop, Bad Cop is the ninth and final case of Layton Brothers: Mystery Room. It investigates the murder of Keelan Makepeace four years prior, and the recent murder of his daughter, Diane. It explains the cause of Alfendi Layton's personality disorder.
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After leaving the room Diane had held her captive in, Lucy decided she needs to locate either Hilda or Alfendi. Lucy began to doubt Alfendi as Diane accused him of murdering her father, Keelan Makepeace. Additionally, the case file (apparently compiled by Alfendi) for the Ham and Cheese case was short of the crucial evidence that would have incriminated Keelan, strongly suggesting that Alfendi had destroyed it.
Lucy made her way towards the base of the West Tower of Forbodium Castle. Upon reaching the base of the staircase, she heard a gunshot. Startled, she quickly made her way up the stairs, discovering Alfendi bound and blindfolded with a pistol in hand, and Diane's dead body lying beside him. Hilda arrived shortly afterwards, quickly accusing Alfendi of murdering Diane and demanding he drop the pistol.
Owing to them being the only people present in the castle, Hilda reasoned that only Alfendi could have killed Diane. However, Al claims that someone else shot Diane, then dropped the pistol in his lap. 'Potty Prof' then makes an appearance, demanding to be untied and insisting that both of the Makepeaces were killed by the same person. Justin Lawson then enters the room, telling Lucy and Hilda to "do as the man says."
After a brief discussion on the whereabouts of the requested back-up, the four decide to begin investigating. Al immediately decides that the only suspects are Hilda, Justin and himself. He retook witness statements from Hilda and Justin regarding Keelan's death four years prior; as he has no recollection of the event, Alfendi decided not to give any statement of his own.
Four years ago, the force was preparing to search Forbordium Castle for Keelan. Alfendi had gone on ahead alone; the raid was called off in favor of Hilda, Justin and the commissioner going after him instead. Justin allocated the commissioner to search the west tower, Hilda to the central tower and himself to the east tower after hearing a gunshot. From east tower's roof, he had seen Alfendi cornering Keelan at gunpoint on the west tower's roof, as had Hilda from a window in the central tower. Hilda reached the west tower first, finding the commissioner trying to break down the stairway door to the roof without success. As the two of them worked together, two more shots were heard from above. When they managed to break down the door and head upstairs to the roof, they found Keelan dead from a headshot and Alfendi unconscious in a pool of his own blood. Justin arrived shortly afterwards. After this recount of the incident, Alfendi and Lucy then begin to search for evidence to clear his name.
They find that, while the gun in Alfendi was holding was used to shoot Diane, the angle of penetration to Diane's fatal wound meant the shot must have been fired from the staircase leading to the roof, meaning Alfendi could not have been her killer. Alfendi then determined that there must had been a secret way to the West Tower roof from another area of the castle, which would explain the killer's escape from both crime scenes. Alfendi also noticed an inconsistency in Hilda's statement; Hilda claimed to have seen Makepeace clutching his right side in agony after Alfendi's first shot at him, though it was his left side that had been injured.
Eventually, Alfendi concluded that the first gun shot heard was not him shooting Makepeace, but rather Makepeace shooting Alfendi, which was why he couldn't remember what had happened. It was also determined that Hilda had lied about seeing Alfendi, as she could not have seen Alfendi from her position in the central tower. She had merely assumed Alfendi was cornering Makepeace from Lawson crying out "Don't shoot, Al!".
After Lucy had failed to determine the secret way onto the West Tower roof, the 'Placid Prof' regained control, then to the apparent shock of the others, revealed that he shot Keelan Makepeace as he remembered himself doing so, upsetting Lucy who then ran away. Catching up to Lucy a while later, Hilda confided in Lucy that Alfendi's real side was really the 'Potty Prof', and that the 'Placid Prof’ Lucy had regarded as normal, was in fact a personality that emerged after the events of four years ago.
Aggravated by the 'Placid Prof' having made a false admission and Hilda's late revelation, Lucy decided to continue investigating on her own.
Lucy headed back to the roof, where she found broken ivy on the rear of the central tower; it appeared as though it was broken by someone grabbing it.
Armed with the knowledge of the broken ivy revealed in her investigations, Lucy and Hilda accused Justin of both murders. Lucy also pointed out something Diane had told her about her father: Makepeace had claimed he could get away with any crime owing to 'friends in the force'.
Lucy presented the original case file compiled by Justin as proof that he had destroyed evidence, and was in fact protecting Makepeace from within the Met. After proving that he must have leaped from the West Tower onto the outer wall of the Central Tower (pointing out that forensics would find rubble, dust, and plant material on anything that came in contact with that wall), and climbed across to the west tower to shoot Makepeace, he confessed to both murders and attempt on Alfendi's life and is arrested.
Some time later, Lucy noted in the epilogue to the case that Justin's arrest prompted the reopening of all the Jigsaw Puzzle cases, where it was discovered that eleven of the twenty-six cases had "nowt" to do with the original Jigsaw Puzzle killer; Justin had planted the jigsaw pieces in order to mislead the investigative team. Alfendi later arrived at the Mystery Room, ostensibly furious; he had arranged a meeting with Justin in prison over Justin's unexplained motives but it ended in a way he found ridiculous. It turned out that Justin had handed Alfendi a 'brainwashing' book that he claimed to have read from during Alfendi's time in hospital while in a coma. Allegedly, this not only created the placid side of Alfendi, but had also implanted false memories within Alfendi that led to him readily admitting (albeit falsely) to the Makepeaces' murders. Both Alfendi and Lucy expressed doubts about the veracity and efficacy of the so-called "brainwashing book", prompting Lucy to remark how it is just a new case for them to solve.In the last scene of the file, the commissioner (who is revealed to be the older Constable Barton) is seen discussing the events over the phone with Professor Layton.
- Ironically, the killing of Keelan and Diane is what saved Alfendi's life.
- Alfendi only came to Forbodium Castle when Diane threatened to detonate a bomb in a school, a hospital, or Lucy's home.
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