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- Unlock all Puzzles in Puzzle University
At the title screen, hold and press , , , , , , , .
- Unlock Very Hard difficulty setting
At the title screen, hold and press , , , , or complete the game under the Hard difficulty setting.
- Unlock Super Hard difficulty setting
At the title screen, hold and press , , , , or complete the game under the Very Hard difficulty setting.
- Game speed over 50 in marathon mode
At the title screen, hold and press , , , , or earn 10,000 points in the time zone.
- Unlock All Trainers
At the trainer select screen, hold on controller 1 and simultaneously press and on controllers 1 and 2, or complete Spa Service.
- Play as Mewtwo
At the trainer select screen, hold on controller 1 and press , , , , , , , , , or complete the game under the Super Hard difficulty setting. Note that Player 2 will always be Mewtwo, while Player 1 is always Ash.