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Knowledge is power and the Doctor knew this all too well. In the wrong hands, entire civilizations could be eradicated or changed in immeasurable ways. In the right hands, it was a tool of enlightenment to spawn creativity, growth and potential. He had this knowledge and he’d used it to both destroy and create. It was a fine line to walk and one which he was perilously close to falling from every day. Companions and friends he traveled with were there not just to entertain or provide friendship but also to be a moral compass. His gob may run and caustic words may spew forth like a waterfall of sarcasm or disrespect, but in the end he knew how close to madness he really was and it was a hand to hold that stopped him from falling off the precipice.
After the war, knowledge was a curse, his burden to bare. He avoided contact with anyone who might show him compassion or solace as he believed he deserved his misery and wanted to fall into the darkness, hoping for death and the end of his burden. The universe would not allow this. The moment his hand touched hers, everything changed. As much has he tried to push her away and run from what she was, is and would become, he couldn’t. She was irresistible to him, his own personal siren whose song was melodious, seductive and a reprieve from the darkness that suffocated him each day. He could see her so clearly and yet she was a mystery as well. For the first time in centuries, all was not clear. This human girl with a simple beauteous name and a smile like a super nova was an enticing enigma that he with all his knowledge and intellect could not decipher.
He knew instinctually that she held some important role and that time moved around her in a pattern unlike other humans. Power swirled around and through her but never seemed to touch her like it did a Time Lord. It was as if she were a ship riding the waves of some ocean, sometimes maintaining course and other times riding the current to wherever it took her but always leaving a wake in her path. The question was, would this wake turn into a tsunami and overwhelm any in her way or would it be gentle waves lapping at the shore carrying with it the soothing sound of the ocean.
Soon, her significance became clarified as he watched her emerge from his Tardis, glorious, terrible and powerful. He was terrified, amazed, fascinated, overwhelmed and filled with love for this girl who had become so much and would become so much more. Even with all his Time Lord training, he never knew completely what had happened to her. Although, he had some theories. Her importance to him was solidified after that event and she forever carried with her the scent and song of time even if she was unaware it. Perhaps one day it would be her destiny to remember and understand what it all meant. One thing was clear, the reverberations of that event shook time itself not to mention what it did to him. Every regeneration thereafter, he would think upon the human girl who swallowed time and every regeneration he was haunted by something, sometimes small or sometimes not so small that was evidence of what she had done.
She was locked away in another universe now. As soon as she had come back and events had unfolded in the Medusa Cascade, it was clear to him what must be done. His choice had been selfless and selfish based on what he knew as a Time Lord was right and what his hearts wanted for her. Part of his decision was assuring her safety and providing her with the chance to become more without the worry of his past sins corrupting or destroying her. The selfish motive was stronger though. There was an inner satisfaction that a part of him could know joy and peace with her, that she would be his and they would have a forever. He suffered through this sacrifice hoping that by doing so, he was assisting her to become what she was meant to be. One day, if he was lucky, perhaps he would learn the full story of the fantastic girl who healed a Time Lord. He hoped she would be happy and hope was a good thing. He always liked hope.