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As this game is a game where you portray a deteective, it's separated by a variety of manners. At the end of each major case, the logbook for human characters, Pokémon, clues and items are reset, indicating a new part of the story. This page details each of these chapters and links to full sections for each of them.

The First Chapter

Locations:
Rhyme City Streets
Tahnti Park

Included Characters:
Emelia Christie

Summary:
When Tim first enters Rhyme City, he notices a group of Aipom stealing a necklace from a young girl, and then his own map. meeting up with a Pikachu, he decides to chase the Aipom and return the jewelry. However, it eventually turns a bit sour when he discovers the Aipom has been attacked in the nearby park.

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The Second Chapter

Locations:
Cave

Summary:
After helping solve the mystery of the stolen items and injured Aipom, Tim & Pikachu return to his father's apartment and find a Key. This key unlocks a cabinet which has a cave map. Exploring the cave, Tim & Pikachu discover Christie and Meiko cowering as a Glalie, with red eyes, turn on them and start attacking. This attack causes a cave in, trapping everyone and it's up to Tim to find out why Glalie suddenly attacked and find a way out of the cave.

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The Third Chapter

Locations:
The PCL

Summary:
After evacuating from the cave, Tim & Pikachu return home and discover a broken Ampoule within Harry Goodman's belongings. With the help of the Detective Agency, they learn that it may have originated from the nearby laboratory, the PCL, and Tim & Pikachu leave to investigate and get more clues to solve Harry Goodman's disappearance.

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Epilogue

Summary:
After solving the clues and revealing the real culprit behind the issues in the PCL, Pikachu and Tim take a break and discuss the fact that Harry is still missing. As they remark on what a good team they make, the game ends with a To Be Continued and Mewtwo flies by...