During the adventure in the Sunken Ship, Amaterasu must use her Celestial Brush to guide the slips from Rao's hand to certain enemies. The ghosts in the ship can only be defeated by Prayer Slips, and they do significant damage to enemies as well. However, there are some things they are unable to damage (like the Crimson Helm and Spider Queen apparitions). After the Sunken Ship quest, the Prayer slips are not seen, used or mentioned again.
- Oddly, although the Prayer Slips belonged to the real Rao and are holy weapons, the eye emblem on the slips is also the windows of the fortress on Oni Island, being a recurring feature.