Prayers follows Jonathan and another young boy named Asuma, who both seek to become Samurai. A mysterious samurai saves them when they were young from the fallen angel Amy.

In the year 1492 of the Gregorian Calendar, in the Eastern Kingdom of Mikado... The Samurai guard the Luxurors and Casualries - the people - of Mikado. The wild Samurai Walter seeks to improve his self-taught, but unrefined skill. The Samurai Gina keeps a close, worried eye on the wild Walter. One night, the pair, while keeping watch, are suddenly transported to an unknown world... There, they see a tyrant - a demon that is far stronger than any they have encountered! As a result of the battle with the tyrant, the fate of this pair begins to shift...!