Harry Potter: The Price of Silence.

Warning: Explicit language, violence and sex.
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In a world where war continues to consume everything in its path, Hermione has become the most formidable warrior of the Order. Dedicated to rescuing Muggle-born slaves who fall into the clutches of Voldemort's followers, her bravery and skills have taken her to the heart of the conflict. For years, she has maintained a secret connection with a spy infiltrated in the enemy ranks, exchanging vital information for the cause.
But when she is captured and imprisoned in Malfoy Manor, of all the dark and evil ways she imagined Malfoy would torture her, she never expected anything so horrific.