Set right after the end of The God Complex.
The Doctor closed the door to the TARDIS behind him. He felt his face relax, as the smile he had hid behind wore off. He had smiled through his tears, to Amy, whom he had just left behind. Again. But this time it was different. Wasn't it? He had left her in safety with Rory to protect her. Brave Rory and brave Amy. And he had left them behind.
He walked up to the control room, up the stairs. His own weight was so heavy - the pain from leaving, from telling Amy - a light in his troubled existence - that he had to leave her and Rory. It pained him to do so. His eyes were stinging, and he looked around the TARDIS, as to see if anyone was there. He realized that he was all alone in his wondermachine; the place where dreams come true and space and time is a formality, was quiet and the lights were low, as if the TARDIS was trying to console him. He let go of his tears and flipped a switch, the noise from the TARDIS' engines filling the room for a while, only to be replaced by a soothing, low humming.
He knows it's important, and that their travels had to end. He knew it was going to hurt, and each time he leaves someone behind, he starts to think whether it's a good idea. As he had once, so painfully accurately said; "they break my heart."
The Doctor walked aimlessly around the console, wiping away tears. Not only had he left two people he loved for their own safety, from him, the monster across all the galaxies, the most feared being in all cosmos, but he knew his death was near. He couldn't run anymore.
His hearts pounded in his chest, a rhythm he usually only felt at times like these. It wasn't the adrenaline pumping, it was the sadness, all 900 years at once, pumping through his veins, making his hearts beat.
He couldn't possibly go back to Amy and Rory now. They deserved to live; to get their chance to live a normal life with a house and mortgage and bills to pay and telly in the evenings. They had comfort in each other.
He knew he didn't want to be alone, so once again, he forced himself to lighten up a bit, and then he set the coordinates to Craig Owens.