The first time he heard her, the Doctor was fiddling with the buttons and levers on the console, having not needed to sleep tonight-he'd slept his share for the week already. When the Doctor heard a panicked scream, he'd realized where it'd come from-from Clara. He rushed to her room, and knocked frantically. "Clara, Clara, are you alright?" When she didn't answer, he opened the door. She was trembling and shaking, her eyes squeezed shut and her breathing quick.
He sat next to her and rubbed her back comfortingly, whispering repeatedly, "It's okay, Clara, it's alright."
Even after she woke up, she never told him about her nightmares. She always kept to herself about them. It was a few months later he heard her again. She screamed, and after hearing it, he realized something. The Doctor was always aware of how Clara would have nightmares, and she'd whimper and scream in her sleep, but something was different this time.
She was awake.