Puppet Princess: Kugutsu Hime. Watashi wa, Ayatsuri Ningyou

On the day of his birthday, Touma Subaru receives a message from his father, Touma Kyouji.
"Come to the school tonight. I've got something for you."
Doing as instructed, Subaru enters a dark classroom. Inside awaits him a single girl - his classmate, Oda Honoka.
From the moment when Subaru rapes Honoka following Kyouji's orders, their ordinary lives take a plunge into the twisted and abnormal as they become puppets dancing in Kyouji's palm...

(Source: VNDB)