Once two armies meet and a battle begins, the game shifts and the player is taken to a detailed 3D battlefield to command formations in real time. The turn based portion has the player using a Risk-like map to manage the clan's economy, conduct diplomacy, and move armies and agents across the islands of Japan.

Total War: Shogun 2 use the same hybrid of real time and turn based gameplay found in previous Total War games. The player takes on the role of one of ten daimyo it is up to the player to lead their forces to victory, and ultimately to seize control of Kyoto to take the title of shogun and restore order. The shogunate lies shattered in the aftermath of the Onin War and the country's various daimyo are warring for scraps of political power. Total War: Shogun 2 returns to Japan's Sengoku (or 'Warring States') period, picking up in 1540 slightly later than the original Shogun: Total War.