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. As the only survivor of an epic battle, he enters the world of Amana, which is currently ruled by Shuzen Fujimori who has overthrown the former superior Lord Sakurai.
The player must decide if he wants to join Fujimori Clan, Ouka Clan (formed by former members of the Sakurai Clan), protect the villagers in Takatana who want peace, or get out of Amana for good. The game offers almost complete freedom to roam the eight zones of Amana while looking over the shoulder of his avatar. The overall story arc allows for over 20 possible endings, which depend on the player's actions and choices throughout the game.
The gameplay is characterized by three options: listen, apologise/beg or attack. Begging a merchant will earn the player a free item but reduce respect from the merchant, leading to less Samurai Points after death or completion of the game. The game features a realistic day and night cycle, which affects NPC behavior and daily life.
The player can interact with various characters, accept different jobs (only one at a time), shop for new items, and engage in mini-games like chopping up vegetables or fillet fish. Decisions influence relationships with the different groups, changing how they interact with the player. The player has access to dozens of swords, hammers, and spears to choose from, each with its own quality and durability level.
The game also features a partnership system, where the player can meet several possible partners who can join him in exchange for money or be "romanced". Partners provide additional combat benefits and unlock access to mini-games and side jobs. The romance with a partner can even lead to them living with the player in Takatane village.