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.