The Church of Saint-Sulpice is known for its eccentric history. It was built over the ruins of an ancient temple to the Egyptian goddess Isis, and was also known to be a clandestine meeting hall for numerous secret societies over the years.
Sister Sandrine is uneasily leading Silas through the church, which is weird because it's so much more interesting in daylight.
Silas is just wishing the Sister would leave him alone. He vowed not to use force unless absolutely necessary, so now he's trying to sweet-talk her into leaving.
He tells Sister Sandrine he wishes to pray, and that she should most definitely go back to bed. She grants his request….at least as far as Silas knows.
She's actually hiding in the choir balcony, watching him suspiciously, and wondering if she'll have to carry out the orders she's held for many years.