- Professor E. Gadd
- Blue Toad, Yellow Toad, Green Toad, Purple Toad
- Shy Guys
- Red Koopa Troopas
- Koopa Paratroopas
- Hammer Bros.
- Fire Bros.
- Boomerang Bros.
- Ice Bros.
- Sumo Bros.
- Monty Moles
The story starts with Bowser thinking about all his plans and becoming mad, because all of them were ruined by Mario and his friends. However, Kamek discovers a new magic, capable of travel between two different dimensions. So Bowser Jr. asks for conquering the world of Pokémon, because with powerful beings as Pokémon are, they can finally kidnap Princess Peach and conquer the Mushroom Kingdom (but this is only a excuse for his real intention: having Pokémon can be really cool). Bowser agrees, because his minions, like Goombas and Koopa Troopas, seems so weak to execute his evil plans. So Kamek makes a protection spell for himself, Bowser and Bowser Jr., starts the magic and put the chemicals in action. But asks for a little patience because of the magic's complexity. Despite of advice, Bowser Jr. decides to put more chemicals in the process, so it can finish faster. Suddenly, everything explodes and instead of travelling to Pokémon World, the two worlds became attached. They realize that Pokémon are now in Mushroom World and only they know what really happened.
A new day on Toad Town, Toadsworth wakes up Captain Toad and Toadette. He says that Princess Peach is waiting for them, so they have to go to find her. After searching in all the accessible castle's rooms, they realize that she isn't there. Toadsworth starts to be really worried, but shows he can't do anything because he doesn't have Pokémon. Toad, Toadette and Toadsworth decide to go to the Professor E. Gadd's lab as he have some Pokémon. In the lab, E. Gadd laughs about Toadsworth's fears. So he reveals a letter wrote by Princess Peach, which asks a Pokémon for Toad and Toadette. Koopa, the E. Gadd's assistant, appears saying the three toads are late and explains that they miss Princess Peach's presence, because she went to investigate some strange happenings on the next city. Toadsworth becomes worried again and asks for the professor to not waste time and give Pokémon to Toad, Toadette and Koopa, so they can go to protect Princess Peach. E. Gadd agrees, but tell them that Peach is one of the kingdom's strongest trainers and doesn't need it at all.
After, the player chooses Captain Toad or Toadette to play with. If Captain Toad is chosen, then Toadette will be his non-playable best friend and vice-versa. Koopa will be their friendly rival. So E. Gadd will asks the player which starter Pokémon he/she wants: Bulbasaur, Charmander or Squirtle. His/her best friend then picks the Pokémon whose type has disadvantage against the type of the player's Pokémon and Koopa picks the last one. The professor also gives them a Pocket Mushdex 1.0 and the kingdom's map. So the adventure begins.
The game starts with Pokémon from generations I and II. The player can unlock more downloading the following packs.
- Pokémon from generation III
- Pokémon from generation IV
- Pocket Mushdex 3.A Update
- Pokémon from generation V
- Pokémon from generation VI
- Pocket Mushdex 3.B Update
Pack 03 or (Pack 01 + Pack 02)
- Pokémon from all generations
- Pocket Mushdex 3000 Update
- Bonus: Fakémon from Fontana Region (after beating the Royal 4)
Note: in the original game, Professor E. Gadd will give a starter Pokémon from generation I in the game's beginning and one from generation II after beating the third gym. If Pack 01 is installed, the player can choose between starter Pokémon from generations I and II at the beginning and from generations III and IV after the third gym. If Pack 02 is installed, the player can choose between starter Pokémon from generations I and II at the beginning and from generations V and VI after the third gym. If the Pack 03 (or both Packs 01 and 02) is installed, the player can choose between starter Pokémon from generations I, II and III at the beginning, from generations IV, V and VI after the third gym and a starter Fakémon from Fontana Region after beating the Royal 4.
This game is compatible with some amiibo from Super Mario collection and Super Smash Bros for 3DS / Wii U collection.
- Using the Toad amiibo will unlock some clothes for Captain Toad's / Toadette's closet.
- Using the Mario, Luigi, Princess Peach, Yoshi, Bowser, Wario, Rosalina & Luma or Donkey Kong amiibo will cause Gym Leaders and Royal 4 giving more money (+20%), after being defeated.
- Using the Pikachu amiibo will allow the player to pick Pichu as the starter Pokémon.
- Using the Charizard amiibo will allow the player to receive a Charizardite X from Mario, after he's defeated.
- Using the Lucario amiibo will allow the player to pick Riolu as the starter Pokémon.