The Doctor watched grimly as the image of the grand luxury starliner on the screen exploded into atoms, with hundreds of souls aboard. No, not souls…puppets. The Daleks had gotten there first. He'd been too late to do anything other than contain the infection - destroy the starliner before it could dock anywhere and disgorge its malignant cargo. He reached up and absently dabbed a smudge of blood off his forehead with his cuff.
He noticed that Clara was still typing furiously at her keyboard. "Clara?"
Her fingers pounded frantically at the keys, and her expression was hollow with horror.
He walked around the console and gently took her hands. "Clara? It's over. You can stop now. You saved us. There's nothing left of the starliner's systems to hack into."
She still stared vacantly at her screen.
The Doctor reached out and cupped her cheek with his palm. He turned her face towards his own. "Clara?"
She shuddered then, violent tremors wracking her petit frame. "All those…people…is that…is that what they did to me?"
The Doctor pulled her in tight against his chest, and rested his chin on top of her head. A single tear trickled down his cheek as he recalled that moment when he'd entered the chamber in the Asylum, expecting to find the witty, clever girl who'd been guiding his footsteps, only to be confronted with a Dalek, in chains. "No, Clara. What they did to you was worse."
"They turned me into one of them?" Her lips trembled, and her beautiful brown eyes overflowed with tears.
"Yes. Yes, they did. But the Daleks underestimated you. They wanted your mind, but they didn't take into account the sheer strength of your will." He tipped her face up, so he could look into her eyes. "You fought them. You hacked into every system on the planet, including the pathweb, which is something not even I could manage. You created a world of your own, inside your own mind, and you were human to the very end. You flirted with me," he added, hoping to coax a smile.
Instead, her face crumbled, and she buried her face against his chest, sobbing brokenheartedly.
"I'm sorry, love," he whispered, wishing that he could spare her this. "I am so sorry…" He winced at that particular choice of words.
"Just don't let go," Clara whispered brokenly. "Don't ever let go…"
The Doctor continued to hold her for a long time after the tears stopped. Finally, Clara pulled back a bit. She touched the large, damp spot on his shirtfront ruefully. "I've got you all soggy."
He smiled down at her and gently stroked her tangled hair back from her face. "It's all right. Tears are gloriously," he kissed her left cheek, "gloriously," he kissed her right cheek, "human." He kissed her forehead. "Feel free to cry as much as you like."
A touch of Clara's usual impishness brightened her features. "Supposing I'd rather do something else?" She reached up and brushed her lips against his, then smiled as he blushed bright red.