The monastery is said to have an underground library filled with many great literary works, such has historical writings and scriptures which includes works of foreign languages. These literary works are strewn in piles of disarray on the floors, and ancient scrolls and lithographs are piled among the printed works. Priests are restricted in going to the third underground floor of the vault. In the deepest area of the vault, the floor covers a tunnel entrance, and a magickal rune is inscribed on the floor.
Five battles are fought in the Monastery Vaults between Ramza Beoulve and the forces of the Church of Glabados. The first three of the five battles are fought in Chapter Three, the remaining two are fought as part of the final sequence of battles leading up to the final boss; it is also the Point of No Return.
Following the declaration of Ramza as a heretic by the church, Ramza attempts to recover the Virgo Stone from the monastery, where Alma believes it to be located. A Templar Knights named Izlude Tingel arrives first, also seeking the stone.
When the monastery's librarian, Simon, refuses to help Izlude he is mortally wounded. Izludeproceeds into the Monastery Vaults to search for the stone and Ramza and Alma arrive to find Simon dying. Ramza leaves all of the Zodiac Stones he had collected up to that point with Alma, and rushes downstairs to confront Izlude.
Isilud finds the Virgo Stone, but is confronted by Ramza. After being defeated in battle, Isilud teleports back up to the exit, where Wiegraf Folles has captured Alma. As Ramza runs back up the stairs, Wiegraf has Isilud take Alma away, while he fights Ramza. Ramza prevails but is unable to prevent Isilud from making off with his sister. As Wiegraf lay dying, the Aries Stone, which Wiegraf had been given by the other Knights Templar, reacts.
A voice offers Wiegraf great power, which he accepts, becoming one with the Lucavi demon Belias. Ramza draws his sword, prepared to fight, but Belias is not looking to fight Ramza just yet, and merely teleports away. After Wiegraf's escape, Simon manages to give Ramza the Germonik Scriptures before dying.