The player is allowed to choose from a selection of different types of puzzles. Initially, the only options are Shadow Puzzle, Motion Puzzle, and Rescue Mission, but after completing 30 puzzles, a fourth variety, Power On, is unlocked. There are 20 puzzles for each type, divided into five levels, with four puzzles to a level. The higher a puzzle's level, the more difficult the puzzle is. Once a puzzle is solved, the Pokémon involved in the puzzle is added to the game's Pokédex, the Minidex.
The player is given a scrambled picture of a Pokémon, and must switch the pieces around to unscramble the image. However, the image is moving, which can complicate matters.
The Motion Puzzles will add the following Pokémon to the Minidex:
The player is given the shape of a Pokémon and a number of puzzle pieces. The objective is to arrange the pieces to form the given shape. Upon completion of a puzzle, the Pokémon it depicts will peek out from behind the puzzle.
The Shadow Puzzles will add the following Pokémon to the Minidex:
The player is presented with a Pokémon that is trapped by a number of blocks. The objective is to slide the blocks in order to clear a path allowing the Pokémon to jump into a hole and thus escape. The puzzles generally require the player to make the Pokémon itself to move around in order to make room for blocks. Some blocks are larger than others, and thus require more room to slide in certain directions.
The Rescue Missions will add the following Pokémon to the Minidex:
Once the Minidex has 30 entries filled in, this type of puzzle is unlocked. The player is presented with a Pokémon's silhouette next to a sliding puzzle. The tiles depict pieces of wire, and must be slid around to connect the ends held by a Pikachu to the ends connected to a light bulb. Once the circuit is completed, Pikachu powers the light bulb, and the Pokémon's silhouette becomes a proper image.
The Power On puzzles will add the following Pokémon to the Minidex: