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The Monastery was lightly damaged during the assault, however the greatest loss was the fact that the Monastery was lost and the passage to the East was blocked by the demon queen Andariel. It was the home to many monsters and one of the lower Catacomb levels was made into Andariel's throne. The Sisters of the Sightless Eye fled the Monastery and made a temporary settlement: the Rogue Encampment. Charsi lost her Horadric Malus while fleeing and tasked the player with retrieving it.
Even though the Monastery was cleaned out by Act II, it still remains deserted even though claims were made by the NPCs that Rogues have been moving back into it.