Way of the Samurai 2 takes place at the end of the Edo period in 19th Century feudal Japan and is set in a town called Amahara, located on the island of Dejima. The citizens of Amahara once lived in peace and harmony, but as policy shifted within the powerful Magistrate's office, they have found themselves the victims of extreme justice. The local 'Aoto gang', who formerly valued love and duty, have become disorganised since the death of their boss. Without a proper leader they have begun to behave without honour, spreading tyranny and fear throughout the town.

• Luckily, change is coming. A lone Samurai warrior arrives in Amahara and over a period of ten days, players must guide the mysterious stranger to his destiny. Little does the Samurai know that his actions over the next few days will irrevocably change the course of the township's history. Whether this change is for the better is down to the choices the player makes. Way of the Samurai 2 has four different plot paths which are linked and decided upon by the conduct of the Samurai and the way he interacts with the people around him.
• Along the way, the Samurai will be asked to complete tasks for the town's people, the Aoto gang or the Magistrates office. It is up to the player to decide which route to take and on which relationships they will risk their reputation. If a particularly controversial mission is undertaken, it will most likely be frowned upon by one of the social groups and this will drastically alter the way that particular group interacts with the Samurai in the future.
• Fight for honour and glory on a quest to free the innocent and destroy the corrupt. Live the way of the Samurai and fight for justice in Way of the Samurai 2.