A/N: More like a series that features 'Saw' than a crossover. Definitely Who enough to rule that out.
"Doctor, what's going on?" Clara yelled above the violently quaking TARDIS, barely able to cling to the rails for support. "I don't know," he yelled back, "but boy you have a talent for keeping a death grip on your tea! Remind me never to try and steal a sip!"
She rolled her eyes. Some things never change. Especially not the Doctor's opinion on her apparent attachment to tea mugs.
The TARDIS landed harshly with a slam and slowly started to tilt to the left. "Doctor!" Clara screamed in alarm. He swallowed and grabbed her hand. "Clara, I don't understand, the gravity-"
Their heads smacked against the metal floor, blacking them both out.
The Doctor's transition between unconsciousness and consciousness reminded him of stirring tea, swirling around and around and around. Finally the spinning stopped, and his eyes adjusted. "Clara?" he called, tensing after hearing no response, but relaxing into the floor when he realised he was still holding her hand. He exhaled in relief as he rolled himself over to cup her face in his hands. "Clara," he whispered, and she stirred gently. "Clara, wake up. Wake up now."
Her eyes snapped open at his urgency. "What's going on, Doctor...?" she slurred, wincing as she tried to sit up but collapsed into his firm grip in the haze of pain. "The TARDIS crashed, and I'm going to find out why. You sit here and recover. Do the human-y heal-y thing."
She nodded silently and happily fell asleep. She must have really hit her head, the Doctor mused to himself. 'Else she'd be fighting for adventure through a concussion and a sprained ankle. It's like an addiction for her or something.
Taking a deep breath to steel himself, he flung open the big blue doors. "Helloooo... I'm the Doc-"
He froze in fear as he watched a very familiar puppet traverse the cold, grey room on a child's tricycle and insert a tape into the player on the table in the middle of the room. The old TV came to life with a haze of static. "...tor..." he finished weakly. An unrecognisable artificial voice began to speak through the dark haze of monochromatic visual static, and the puppet stopped to stare at him.
"Hello Doctor. I'm sure that, as a delightfully experienced time traveller and well-learned man, you know who I am. As you also know, your beautiful little companion Clara is sleeping inside the TARDIS, recovering from her fall. She's died many, many times for you – far too many, in fact. I've overridden the main protocols to lead you here, and your little box is currently in a state of panic. I'm sure you know what that looks like. You have fifteen minutes to find your companion before the doors seal, locking you in this room. If you do not find her within the time limit, this room will explode, taking your TARDIS with it. Dark Star Grenades, Doctor. They will eat up your TARDIS like a breakfast treat.
So, Doctor – will you let her die for you again? Live or die, Doctor. Make your choice."
He shuddered, and covered his ears with his hands, breath becoming something of a difficulty. For four hundred years he'd buried this memory. That voice had only just stopped giving him nightmares. A shot of Clara lying still on the floor, somewhere in his beloved TARDIS flashed across the screen. Fear and regret that he'd ever opened the TARDIS doors consumed him, but somewhere within himself he found the courage to whisper, "Let the games begin."
The Doctor pushed open the doors with a big breath and ran inside, only to find that he was in the middle of the library. He rolled his eyes at his machine. "Of all times..." he muttered under his breath as he ran the length of the aisles, took a right, and ran straight across until he reached a very familiar hallway. The same hallway structure of all the hallways in the TARDIS. Anxiety struck him as he looked around frantically for clues of her presence. He'd never find her, not with the TARDIS changing the interiors every five seconds. Then he heard a blood-curdling scream from just down the corridor.
There he found Clara gasping for air on the floor, clutching her heart-shaped face in fear. "Doctor?" she called, looking up at him in hope. He fell to his knees before her and held her close. "Clara," he whispered simply into the place between her neck and shoulder, before pulling back to the sight of half her face missing. Blood had already congealed around the raw flesh and cartilage, and the Doctor barely managed to stagger backwards before retching violently on the floor. The TARDIS made a shuddering wheeze-like noise, halfway between her own fear and condoling him. All this usually advanced Time Lord could do was lie there and quiver in disbelief. It wasn't the gore; it never was. He was a soldier and a doctor – he knew what that looked like. He was the universe's John Watson, and someone had attacked his very own Mary and taken half her face.
The thought alone made him positively livid.