The game takes place on the Lental region, where the protagonist arrives to assess the region for an ecological survey. The player meets Professor Mirror and his assistant Rita. Later on, they meet their rival Phil and his mentor Todd Snap, the protagonist of the first Pokémon Snap.
In the game, the player takes photos from the NEO-ONE vehicle, which moves along a set path. The player's main goal is to take good pictures of the various Pokémon living in the different biomes. As the game progresses, the player unlocks new tools to help them take better photos. The player can throw Fluffruit, which some Pokémon will eat. Illumina Orbs will briefly cause a Pokémon to glow, but they must be unlocked for each region in the game. The player can also run a scan, which will make identifying nearby Pokémon and discovering secrets easier. The melody button plays a brief song that certain Pokémon will react to. Finally, the player earns the ability to move the NEO-ONE faster than normal.
The game features a variety of tasks that test the player's photography ability by making them snap a picture of a certain Pokémon, usually performing a specific action. For instance, one challenge involves befriending a Pidgeot by feeding it Fluffruit twice on the route.
- Shroomish appears in the game's files, despite not actually appearing in-game.