Using the run-down hut as a base-of-operations, Goh must locate the stones to reclaim his memory and discover the truth regarding the destruction of the Asuka ninja. The letter informs Goh that his memories and soul have somehow been stolen and placed within eight mystical stones which were scattered during the initial attack on the Asuka ninjas' village, and then further scattered by people who have located and claimed the stones. The letter states that the person who wrote it is simply a 'concerned bystander,' and further identifies the amnesiac man as 'Goh,' a ninja of the Asuka clan, which was wiped out the previous day. Startled, the man scans the trees and undergrowth surrounding him, but then notices a letter attached to the arrow. Finding only a sword lying next to him on the ground, the man stumbles across an isolated and seemingly derelict shack, only to have an arrow shoot past his head and lodge itself into the shack's outer wall. In fact, everything is unfamiliar, as the man finds that he can no longer remember his identity and has no memory of his life or situation up until the point of his regaining consciousness. Shinobido has the player take the role of an amnesiac ninja who wakes to find himself lying on the bank of an unfamiliar river.

Shinobido ps2 iso