AN: Spoilers for LOTL - since it's the TARDIS thinking and healing after the events that happen within it. Do leave a review if you should feel so inclined.
It Still Hurts
She's still healing, even now. He had cannibalised her, and laughed at her screams of agony. She had never known such pain. The paradox ripped her apart, healed her briefly, and then ripped her apart all over again. She had thought that losing her soul sister would have been the worst pain she would ever face, but being broken while you were still fixing yourself... It had proved her wrong.
What had happened to her dear little Koschei? What had he become? Sometimes, she briefly caught a glimpse of him, and it would spark hope, but then the Master would return, and Koschei would be little more than a memory. It was only when he laughed at her pain that it really sank in. Her Koschei was dead, long dead. All that remained was the Master, and she hated him.
But oh... it hurt so much to hate him. She would think of him, during the brief periods of healing before the paradox ripped her apart again, of Koshei and Theta, the little peas in a pod she loved so much. Theta still remained, well hidden, most times, but she knew he was there, and quite often he came through.
His anguish and anger at what the Master had done to her was what really hurt, and hurts even now. She didn't know how two so similar could become so different┘ It was like her and the Bad Wolf becoming sworn enemies - unthinkable to her.
She had cried out many times for Bad Wolf while the Master caused her pain. He would snap at her, tell her not to talk such rubbish, that the Bad Wolf was only a myth, and whenever he did, she would zap him with whatever strength she had, defending her soul sister. Just a myth.
Was it a myth that healed a TARDIS' soul?
Was it a myth that ended the Time War?
Was it a myth that the Doctor owes his life to?
Was it a myth that saved the world?
What she wouldn't have given then for the courage of the Bad Wolf.
It still hurts. The loss of a soul sister, the loss of Koschei, the pain of the Doctor, her little Theta, and she herself still hurts from the paradox machine. It hurts to look at Jack, and know what will become of him, and know why.
It hurts so much, and Theta isn't strong enough to help her.
But with a (metaphorical) smile, she knows she has one lifeline. She may have lost all she needed to heal, but she didn't lose hope.
After all, even though she stayed behind, she's still got her medical Martha Jones, and a promise.
And for now, that's enough.