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At the Thwomp House, he arrives to solve the crime of who stole forty of Thwomp's coins. After looking over the house, it is revealed that the door was too small for Thwomp to leave, meaning there was no robbery, as he couldn't possibly have left. Thwomp says that he was lonely, and that he reported the crime because he wanted to be cared about. Shroomlock then decides not to arrest him, becomes his friend, and leaves to solve the next crime.
At the Ukiki House, Shroomlock arrives after having heard a report about Ukiki being stolen. Akiki, who was at the house at this time, gave him a note that actually stated where he was. He then gives the player the quest of finding Ukiki.
At the Bowser Mansion, Shroomlock is present already, having been given the assignment of finding the missing paintings from the museum. After listening to Bowser's alibi and listening to what he says about the mansion and painting, he and the player discover that Bowser was lying about his mansion; he couldn't have known he couldn't hide the painting in the mansion unless he had seen it, which proved that he had stolen it. Koopa Kid then leads him to the location of the painting.
At the Boo Cemetery, The Boos have had their golden Boo statue stolen, and Shroomlock arrived after hearing a yell. However, the Boos then notice that there are four of them, and Shroomlock figures that one of them had stolen the statue and was a fake. After the fake Boo is discovered, he reveals himself as Koopa Kid and flees, leaving Shroomlock to follow him.
At the Sushi Cliff, Shroomlock was pulled into the sea by somebody, and finally emerges after leaping off a sea sponge. Sushi, who was nearby, had interviewed Blooper, Cheep Cheep, and Dolphin, who were at the cliff at the time the crime had occurred. After listening to the alibis, the player figures out that it was Blooper who had pulled him in; Shroomlock explains to Blooper, who had arrived at that moment, that he was the one because none of the other suspects had arms to grab with. Blooper apologizes, and Shroomlock forgives him, leaving to find another crime.
At the Koopa Bank, Shroomlock arrived late due to his car being wrecked. Koopa explained that the lights suddenly went out, and then when they went on, all the coins in the safe were gone. Koopa lists the three suspects and Shroomlock sends the player to talk to Goombob, Paratroopa, and Mr. I. Goombob said he heard the safe open. Paratroopa said he saw a gleam of coins. Mr. I said he heard coins jingle. It turns out that Paratroopa is guilty because he couldn't see anything in the dark. Paratroopa then arrives and admits he is guilty. Koopa asks Shroomlock to let Paratroopa go, because it was just a prank. Shroomlock states that Paratroopa had gone too far this time, but nevertheless complies, albeit reluctantly.
The ending of the game states that he had gone on vacation, and solved a crime there.
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