The main-series leveling system is replaced by a concept called "link", a percentage which increases to a certain maximum, and reflects that Pokémon's battling statistics.

Almost all 200 Warriors in Pokémon Conquest are based on a real historical figure from the time of the Sengoku Jidai - Japan's Warring States period.

37 of them stand above the others as Warlords who are distinguished by having gold icons, unique sprites, individual post-game stories, and being able to transform (becoming stronger in a similar manner to Pokémon evolution).

Warriors and Warlords all over Ransei sought to fulfill the foretold legend, resulting in battles and an end to the region’s peaceful era.

Hideyoshi of the nearby kingdom of Ignis (カエン, Kaen) sends his warriors to ambush Aurora, only for them to be defeated by the player and Oichi.

After conquering the two kingdoms of Terrera (ダイチ, Daichi) and Illusio (ゲンム, Genmu), Oichi hosts a celebration of Shingen and Kenshin's recruitment to the player's army.

During the celebration, the player is confronted by Nobunaga, who holds the kingdoms of Avia (ツバサ, Tsubasa), Cragspur (キガン, Kigan), Yaksha (ヤシャ, Yasha), Viperia (ドクガ, Dokuga), Valora (フクシ, Fukushi), Nixtorm (フブキ, Fubuki), and Spectra (ミタマ, Mitama) under his command.

After linking with Arceus, the player is confronted again with Nobunaga, now partnered with a shiny Rayquaza, along with Mitsuhide, Nō (ノウヒメ, Nouhime), Ieyasu, Ranmaru, and Hideyoshi for a final battle.

However, seeing the player unaffected by being linked to Arceus, and as the Pokémon takes its leave, Nobunaga relents; Ransei's kingdoms are restored to their proper owners and a system in the region is established.

They feature smarter AI (with the opposing nations attacking your countries more often), and the ability to upgrade the locations within the regions through a bank to find more Pokémon or get better items and to evolve the rest of the Warlords.

[18] IGN gave the game a score of 9 and an Editor's Choice award, praising its deep gameplay and calling it "one of the greatest, most fully realized Pokémon spinoffs in existence".