As with all previous Pokémon Mystery Dungeon games, you play as a human who has been turned into a Pokémon and sent into the world as that Pokémon. While the previous game decided on the Pokémon by selection, this game allows for you to choose your Pokémon through various questions, as per the original Dungeon games.

There are 20 different Pokémon to choose from for both you and your partner, allowing for more variety compared to the game's predecessor, but there are restrictions on what is selected as your partner, but you can bypass these restrictions. If you select a Grass-type Pokémon, you'll get a Water-type, Riolu or Pikachu
If you select a Fire-type Pokémon, you'll get a Grass-type, Riolu or Pikachu
If you select a Water-type Pokémon, you'll get a Fire-type, Riolu or Pikachu
If you select Riolu or Pikachu, you'll get Chespin, Fennekin, Froakie, Pikachu or Riolu.