Hinata was used as a human experiment by Danzo and his scientists

Hinata, having ravaged by Danzo and his men, soon broke down into insanity. Danzo tried to brainwash her into one of his own, but she resisted it as she was deeply in love with Naruto. He considered to let her act as a plaything and a puppet for his group, but he gave up the idea as Hinata was simply too weak to withstand continued sex.

He decided to do some human experimentation on the Hyuga princess. She had a surprisingly strong willpower and as the heir of Hyuga clan, she also had a strong body and inner strength. Danzo decided to make her a human subject for his sinister experiment.