In Pokémon Conquest, players take on the role of a young Warlord who is linked with a Pokémon. Together, they must set out to recruit Warrior allies to strengthen their growing kingdom. Along their journey, players will encounter a variety of Pokémon, as well as Warriors and Warlords inspired by the Japanese feudal era. The game contains nearly 200 Pokémon, including many from the recent Pokémon Black Version and Pokémon White Version games.

As the battlefield unfolds in Pokémon Conquest, players must choose the correct Pokémon type to inflict maximum damage on their opponents. In the turn-based skirmishes, players choose different tactics for intense six-on-six battles, and battle conditions can change on every turn, keeping players on their toes in anticipation of what will happen next.

New features in the game for players to conquer include:

Story: To save the Ransei region from Nobunaga, a powerful Warlord who is trying to take over Ransei, players must conquer different kingdoms to strengthen and grow their own kingdom. There are 17 kingdoms in total to conquer. Conquering all 17 kingdoms and ultimately uniting the kingdom will awaken the Legendary Pokémon and save the land from destruction. Story mode is organized by episodes. Players unlock episodes as they progress and each episode features a different playable Warlord and victory conditions.

Army Mechanics: Players can grow their army by recruiting defeated Warlords and their Pokémon. After a kingdom is conquered, players will also have access to the kingdom facilities such as training grounds, shops to buy items and mines for money. Players can also strengthen their army by linking with Pokémon. Warlords can have various linked Pokémon and switch between them before battle to strategically prepare for the type of battle they are about to engage in.

Battle Mechanics: Players will encounter a wide range of battlefields as they progress through the game. Each of the 17 kingdoms has a different type-themed battlefield. For example kingdom Ignis is fire-themed and has lava flows, lava beds and fire spouts for players to battle around. Strategically using water-type Pokémon to navigate through this battlefield will help players conquer this kingdom. Additionally, players can use the kingdom training grounds to train their army or find wild Pokémon and link with them. After battling with a Warlord, the game automatically registers them. Using the built-in local wireless connection on the Nintendo DS, players can battle with friends who also own the game with their registered armies.

Warlords and Pokémon: Each Warlord has a special ability that can change the tide of battle. For example, Warlord Oichi has the ability to heal all the Pokémon in your army. Warlords also have types much like Pokémon. This will determine how well they link to particular Pokémon. Some Warlords will have the ability to choose from several different kinds of Pokémon to link with.