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On the game, an exclusive type makes a appearance: Ninja type. The only Pokémon on the game that it's Ninja type is Accelgor, Greninja and Ninjask. On the game, two worlds are able to travel.
Along with Oichi and Jigglypuff, the Player and Eevee were on Aurora resting at night when they defeated Nobunaga's army. Three months later, two warriors invaded the lovely kingdom and wanted to battle. When the Player and Oichi defeats them, they follow the warriors and discover a new kingdom named "Magnis". Then the adventure begins.
- Magiry (8 kingdoms)
- Vallenin (9 kingdoms)
The gameplay is very similiar to Pokémon Conquest. But now, the sequel has new features in a Kingdom Battle. When you choose fight, A "choose a move" screen appears in the hereinafter screen. This game is now compatible with other Pokémon games by connecting with another Nintendo 3DS on Pokémon Bank.
- New Game
- Continue Game (Only appears if you has a Saved Data)
- Local Multiplayer
- Stage Builder
When you conquest the first kingdom and return to the main menu, you unlock Stage Builder mode. There you can create your own level and battle with CPU. Besides, you can share it too. When you conquest different kingdoms, you unlock parts for Stage Builder.