It's been three months since the Sacred Sword War ended, & Kojiro and Ryoma are nowhere to be found. Back at the villiage of the Fuma clan, a group calling themselves the "Shinsei Fuma clan" forms, calling for an end to the clan of old... And those who are not with them are considered the enemy.

It is the beginning of the industrial revolution, and feudal Japan is in turmoil. The ruling Shogun are wielding their abusive powers to instill fear and dominance over their oppressed subjects. Beatings, imprisonment, rape and even murder are the adopted tactics chosen to maintain their reign. The bloodshed must end. A group of Samurai have banded together, and, with the development of new weapons and new technology, they have both the will and the hardware to stand up and fight. Ichimatsu is one of these fighters. By day, he works incognito at a local tavern, in the evenings he frequents the brothels, and by the dark of night, he doles out some big-time, gun-barrel justice. He is here to help. He is Samurai Gun.

Two partners Effera and Jiliora escape from a slave boat with the aid of their friend Orlin and a young boy named Kilian. When Kilian is killed in the escape Effera and Jiliora take it upon themselves to return Kilian's pendant to his two siblings who are being held captive by Baron Celdion, who is plotting to take over all of the neighboring countries.

1800年的日本，活跃着一位头戴黑色假面的男子，他使用着新式的强力武器——“侍铳”。由于他一贯疾恶如仇，所以平民百姓称他为义贼。事实上，他真正的身份是幕府的敌对势力“养成堂”秘密培养的战士，拥有超常的耐力与反应速度。在风云动荡的幕末，在一场场险恶的战斗中，包括主人公在内，所有人的信念都经受着前所未有的考验！