He was standing aboard the Valient looking out the window onto an Earth that was none the wiser about the events of the last year. To them it was just a normal day, though the president had still been killed, the citizens lives would go on as normal. Behind him on the ground lay the man responsible for it all. He had let the bullet kill him rather than take responsibility for his actions.
He turned to head to his TARDIS. He had to fix her from the monstrosity that the Master had turned her into. Jack had all ready gone ahead of him to begin the work, but he couldn't do it all by himself. The Doctor couldn't bring himself to look at the Jones family huddled together at the bottom of the stairs. Martha was among them and though he hoped she would continue to travel with him, he knew in his hearts that she would stay with her family instead. In a way he was relieved, he didn't want to talk about what happened, and she had a way of getting him too.
He walked over and picked up the body of his friend. It was only just cool to his touch and rigor mortise had yet to fully set in. The Master didn't deserve the traditional burning of the body, he had disgraced everything it meant to be a Time Lord. Still at one time, the Master had been his best friend and close enough to be his family. He carried the body on to his TARDIS and dumped it unceremoniously off to the side near the door.
"Are you going to be all right Doc," Jack asked him in concern.
"I'm always okay," He answered as he examined the controls. Yet even as he said it, he knew it was a lie. Dip in the pit of his stomach, something still felt wrong. He stroked the controls of the TARDIS comfortingly and felt her hum through him in return.
"We'll fix this old girl." He told her and Jack nodded his agreement. It was late into the night, and he was exhausted by the time the TARDIS was back to her old self. He wanted to crawl into bed and sleep for the next year but he still had work to do. The Jones family had been taken home by the military, so he dropped Jack off at Torchwood before choosing a secluded place near a lake.
He built the pyre using loose pieces of driftwood from the lake and logs that he kept in the TARDIS for his fireplace in the library. He laid the Master's body upon the pyre and looked at him.
"I hope you have finally found peace from your madness. I fear mine is just beginning." He told the body. He lit the four corners of the pyre.
"I return this body to the sky and the earth," He whispered, following the ancient traditions. He had always hated them, but now with Gallifrey being gone, something about it just felt right. As the flames overtook the body he turned and headed on to the TARDIS and to his room. Tradition stated he was suppose to stay with the body until the flames burned out, but he couldn't bring himself to stay.
In the morning he would get Martha and go make sure Jack was okay, but for now he just wanted to be alone. He crawled into bed, it had been so long since he had slept in comfort that he was quickly asleep. Unfortunately even the TARDIS couldn't stop the nightmares. In his dreams he was back aboard the Valiant and laying on the bed with his hands and feet tied together.
"Please stop. You don't have to do this." He begged the Master. The Master ignored him as he flipped the Doctor onto his stomach.
"Why," He asked in one last attempt to understand before his world was filled with pain again.
"Because you're mine." The Master laughed. The Doctor woke up in a cold sweat as his stomach flipped he barely managed to roll over and lean off the side of the bed before he threw up. He groaned miserably as he rolled back towards the middle and lay on his back. It wasn't the first time a nightmare had made him sick and he knew it wouldn't be the last. Yet unlike previous times he drifted again off to sleep.