Todd Snap (トオル, Tooru), a Pokémon photographer, is summoned by Professor Oak to Pokémon Island, a place with a variety of climatic and geographic regions where Pokémon live relatively undisturbed by humans. Oak needs quality pictures to accompany his scientific findings and knows from past experience that Todd is the right person for the job. Using a motorized, amphibious buggy named the Zero-One, Todd explores the island and takes photographs of the wide variety of Pokémon that inhabit its environments.
From Professor Oak's research hub, the player can select between the game's levels and features using a menu system. The Zero-One follows a linear path throughout the level, similar to a rail shooter. Up to 60 pictures can be taken per visit. After completing a course, the player selects their best photos of each Pokémon to be rated by Professor Oak and added to the Pokémon Report. Scoring takes into account various aspects of the pictures, such as the Pokémon's size, its pose, and keeping the Pokémon in frame. Extra points are awarded for capturing a "special" pose or Pokémon, such as a surfing Pikachu, and if there are multiples of the same Pokémon within the frame. Scoring well in the Pokémon Report and photographing a wide variety of Pokémon is required to make progress in the game. Players can also use an "Album Mark" to bookmark their favorite pictures; this adds the pictures to a personal in-game album to view at a later date or show to friends.
Players start out with only a camera, but as they progress, Professor Oak will provide them with a number of special accessories used to obtain better photographs. The game features seven levels: Beach, Tunnel, Volcano, River, Cave, Valley, and the special course "Rainbow Cloud". However, the staggered acquisition of accessories ensures that the player must re-explore the courses to discover new material. Levels must be replayed after acquiring new accessories in order to locate hidden Pokémon, alternate routes, or photographic opportunities that yield the best scores. The first accessory, apple-shaped Pokémon food, can be thrown to either stun or attract Pokémon. Another, "Pester Balls", are able to knock out Pokémon or flush them out of hiding. The Poké-Flute object is used in a variety of ways, such as awakening, irritating, or hatching Pokémon. It can also cause Pokémon to dance, and it can play three different songs, resulting in different dances from certain Pokémon. Additionally, players can obtain a Dash Engine for the Zero One, allowing the vehicle to accelerate and move faster than normal.