The main part of the game is the Pokémon Storage. Here, you can store Pokémon in up to 25 different boxes. Each box can store 60 different Pokémon allowing for you to store up to 1,500 Pokémon. You can mass transfer Pokémon from the GameBoy Advance games by controlling the game with the GameBoy Advance.

There are some restrictions:

Pokémon Ruby, Sapphire & Emerald:
Must have the Pokédex to deposit
Must have 100 Pokémon registered in the Pokédex to withdraw Pokémon added from other games

Pokémon FireRed & LeafGreen:
Must have completed Celio's quest to get the Ruby & Sapphire for the machine in the One Island Pokémon Center
Must have 100 Pokémon registered in the Pokédex to withdraw Pokémon added from other games

Within the Pokémon Storage, you have the ability of checking out the Pokémon's stats. This includes all moves, abilities and Contest stats. You also have the ability to search for Pokémon through this feature.

In the game, there is also the feature of looking at your Pokémon collection. This is done by converting each Pokémon into a figure, with the sprite of the Pokémon sitting atop. These can then be organised how you see fit and you can take photos of the collection.

Once the photo is taken, then it can be used as a wallpaper for the boxes.

Previously a feature in the Pokémon Stadium games, when you have Pokémon Box loaded and connected to Pokémon Ruby or Pokémon Sapphire, you have the option of playing the game on the TV. Unlike the Pokémon Stadium predecessors, there is no "Doduo" or "Dodrio" mode to allow you play at increased speeds, but rather it just allows for you to play at the standard speed.

You may also control the game using the Gameboy Advance as a controller.