Clara has awoken on the floor of the TARDIS console room, the Doctor staring down at her. The tension of betrayal pollutes the still air.

Her bloodied lips were parted in an unforgiving O, trembling with either emotion or as a product of her physical state, he didn't know. Didn't care. He was jesting, he didn't really mean…would never…

The Doctor's thoughts flew broken within his supreme, timelord mind, at a loss for what to do. His mouth opened and closed, his voice hesitant to work properly. He licked his chapped, thin lips and broke eye-contact, staring at the grated floor in shame. Clara's ragged panting was the only sound in the room. Even the TARDIS had ceased her usual groans and whines.

In a small, low voice, the Doctor croaked, "Clara, I-"

"Can we do this later? Please?" she managed, cutting him off in shallow gasps. He crouched beside her and set her left arm gingerly around his neck. The pain in her voice was enough to cause fresh tears to burn treacherously in his eyes. His Clara. With one arm around her back and the other clutching her hand, the Doctor hauled her to her feet with a grimace. Regret and sympathy weighed down his hearts so much he thought they'd stop beating. The small human cried out whenever her arms were moved or her entire right side was touched, limping along towards the corridor with his help…she winced with every step. Each time the pain became too much to bare, he'd rub his thumb affectionately against her hand and hush her softly.

Turning slowly into the first room (compliments of the TARDIS), the lights flickered on. Not that it made a difference anyway. The room itself was pitch black, with a single silver medical table in the center of the room. Clara was visibly crying by the time the two made it to the table. As she lost her battle of containment, he helped her onto the table and held her face in his hands. Wiping her tears with his thumbs, he gazed into her battered face. Scratched and dust-covered, beaten and broken, scraped and torn…and his Teach had sustained a strong demeanor, not faltering for so long. Her eyes locked onto his for a moment before his previous words re-entered his mind. His gaze faltered, he closed his eyes, and leaned forwards. Resting his forehead on her brow, he raised his hands to the sides of her head. Ignoring the blood beneath his fingertips, he stroked her hair behind her ears and gently touched her temples.

"I'm sorry, Clara. I'm sorry I failed to protect you yet again. I'm sorry I said…" his words caught in his throat before he swallowed and continued, "I didn't know," he rumbled. Reaching into her mind with his own, he walked among the dull glows of aches and the lightening stabs of pain her nerves were experiencing…soothing them the best he could, he felt a small sigh of hot breath wash over him. An uneasy weight appeared as a lump in his throat as his grip of her consciousness lessened. Not the simple, awake-or-not consciousness, but the spark of life and being itself. It was shockingly, frustratingly weak. Retreating with uncertainty, he willed her to lay down and rest on the metal slab of the black room. She trembled on the table, a great shudder racking her body as another tear rolled down her tear-streaked face. Striding deliberately out of the black room, the Doctor flipped a switch and closed the door, peering through a pane of glass.

Lying in the dark, Clara's pain reduction was lulling her into an exhausted sleep. Eyes open in futility, she gazed blankly into the blackness. Her mind devoid of thought. She simply existed. The static of a com device intruded the peaceful silence. "pssshhhhClara, I need you to stay awake just a tad longer. I'm releasing the nanogenes now. Hold on a bit longer. Use that damned stubbornness…

do not go gentle into that goodnight."

A soft golden glow appeared above her, humming minutely in a soft monotonous tone. Beads of the light separated and swirled down to her, twisting into wide helices and spiraling in an entrancing dance. She inhaled steeply, adoring the light and wishing to see their majesty…but a far more pressing matter overcame her. A memory spilled forth from the recesses of her mind, a memory of a thousand and one emotions. A memory wrapped around the dying of the light.

A soft smile curling the corners of her cut lips, she breathed, "Run, you clever old man…" The Doctor's hearts froze behind the door. "CLARA!" he roared into the com. Flooded with emotions he couldn't begin to describe, he pounded his fists against the door, the anger and sadness and regret and shame and loss exploding within him. Slamming both fists and head against the door, he felt his nose become wet and cool. He didn't care. His TARDIS whined at his self-inflicted punishments and the frailty of those strays he insisted on caring for, on making their ephemeral lives more thrilling.

The nanogenes were upon Clara now. Lighting up her entire body, they set to repairing the flesh. She felt muscles knit themselves back together in an uncomfortable mesh, her skin literally crawling back into place…her words persisted: "…and remember…" The Doctor pummeled the door again. If he entered the room, the nanogenes would become confused, unsure whether he was a mutated human or she a damaged timelord, whether they were two species or one. It was dangerous for the both of them…

A proposition stark as lightening flashed through his mind as he rested his head against the door, panting. A damaged timelord…

She could stay with him, this way. For as long as time itself. Bewitched by the exhilaration of a rash decision, the Doctor rushed forward into the door again, screwdriver ready to magnetize the seal- but the TARDIS would not allow it. He threw himself headlong into the door, and found himself inside of the control room, staggering to regain his footing. He stood, threw his head back, and cursed the TARDIS. "Let me DO this!" he bellowed.

Skidding back to the nanogene-door, the Doctor's head cleared, his anger dissipating at the sight of the marvel before him, through the lens of the icing-glass window.

Clara's form was engulfed in the golden particles of light. Nanogenes swirled around her and through her, the golden bits of light doing their work admirably. The sight was beautiful. Hope blossomed from the ashes of sorrow and anger, and he stepped closer to the glass. His soul a phoenix, he waited with bated breath, returning his screwdriver absentmindedly. Stroking the battered door frame, he whispered, "Sorry old girl. You were right."

The light of the black room ceased to exist in a flash of darkness.

Rage, rage against the dying of the light.

The door clicked open, its despairing echo ringing restlessly through the black room.

Do not go gentle into that goodnight.

A shaft of pale light shone from the open doorway. A stray nanogene disappeared through a vent, the fireflies having given up or emerged victorious. In the very least, it was finished. In long echoing steps, the Doctor walked along the shaft in a century's worth of time. His slim shadow cast before him with each step, its steps echoing as his echoed…perhaps his only companion now…joints trembling with anticipation and dread, the Doctor brought himself to her side slowly. Soft lights flickered on from an unknown source, casting odd shadows about them.

There she lay. No gashes, no stringy muscle, and no tears. Brushing an out-of-place lock of brown behind her ear, he saw her breathe in deeply at the contact. The breath of consciousness—supplying oxygen to her brain and heart and bloodstream and his own hearts too, it seemed. Her eyelids opened languidly, and he drank in those warm, cinnamon eyes of familiarity and comfort.

"Have a nice nap?" he inquired, his Scottish burr reverberating through the walls.

And this is it. I'd be glad to answer any questions about the chronology of everything

I hope it was to your liking :)