Way of the Samurai 3 follows the same principles as its predecessors, offering an authentic setting, a deep sword-fighting system, and cause-and-effect role-playing. This time around, the game takes place during the Sengoku Period and puts the player in the sandals of a lone samurai who is the sole survivor of an epic battle. The new ruler, Shuzen Fujimori, has overthrown the former superior Lord Sakurai and rules Amana with an iron fist to maintain control.
The player must decide whether to join Fujimori's Clan, Ouka Clan (formed by former members of the Sakurai Clan), protect the villagers in Takatana who want peace, or simply leave Amana for good. The game offers almost complete freedom to roam the eight zones of Amana while looking over the shoulder of the player's avatar. The overall story arc allows for over 20 possible endings, which depend on the player's actions and choices throughout the game.
During gameplay, the player has three options: listen, apologise/beg or attack. These choices affect the respect the merchant has for the player and the Samurai Points earned after death or completion of the game. The game is divided into different scenes with possible next ones marked on the in-game map, making it easier to follow.
The game features a realistic day and night cycle, which affects the NPCs' ordinary lives even without the player's interference. The player can talk to various characters, accept jobs, shop for new items, and participate in mini-games like chopping vegetables or fillet fish. Decisions influence relationships with different groups, changing how they interact with the player.
The game offers a wide range of swords, hammers, and spears to choose from, each with variable quality and durability levels. The player can perform both offensive and defensive moves depending on their fighting style and unlock special actions. They can also decide whether to kill someone or use a blunt weapon, which affects the reputation and future encounters.
During the course of the game, the player will meet several possible partners who can join them or be "romanced". Partners offer an additional edge in combat, access to mini-games and side jobs, and even living arrangements. The romance can lead to the partner deciding to live with the player in their home in Takatane village.