A/N: These are some thoughts I think the Doctor could have been having after "A Good Man Goes To War". Some of the stuff comes from the extras on the Series 6 Boxset, 5 short episodes called "Night and the Doctor". It shows what the Doctor gets up to while the Ponds are asleep.
Hope you enjoy!
Simple
He had let them down. So badly. He didn't know what to do. They were his best friends and he had failed them. Melody was lost to them now. Someone else would see her grow up, teach her what was right and wrong, and they would definetely teach her wrong.
He couldn't find her. He had tried, he really had, but he didn't know where else to look.
When he had found out Melody was actually River Song, he had been elated. He had started to have some big, scary feeling towards River and to find out she was the daughter of his best friends made him feel so relieved. But it also frightened him, Rory could do a lot of damage with the pointy end of a sword and the Doctor did not want to be on that end.
He had left straight after he had found out River's true identity. He didn't know where exactly he was going to go but he had to leave Demon's Run. He had a lot of things going on in his head and he felt like something big was going to happen very soon.
He felt so sad for Amy and Rory, they had had their baby taken away from them only hours after they had met her. He couldn't imagine how Amy felt. She hadn't even been on the Tardis for months. He had noticed it wasn't the real Amy quite quickly. It had taken him a while to prove anything but it just wasn't her. He knew her like the back of his hand and after all their travelling together, he was bound to notice if something wasn't right. He didn't understand how anyone had got the real Amy, and that worried him. He always understood things, and for someone to be able to get onto the Tardis without him knowing scared him.
As soon as he had got in the Tardis he tried to track baby Melody down. He owed it to Amy and Rory, he had to try. He had looked everywhere, any hint of Melody he could find but whenever he looked she would be gone. Eventually his Tardis would just take him to Stormcage, to River.
Whenever he felt down, he would visit River, she always cheered him up and she never said no to going galivanting around on adventures.
Before Demon's Run, while they were still on the Tardis together, just the three of them, he would sometimes go to Stormcage, at night, when the other two were asleep. It wasn't that he got bored of the Ponds but he didn't have to sleep as much as them and he needed something to occupy his nights. River would always be waiting for him. Whenever she heard the Tardis materialise outside her cell she would be at the bars instantly. Waiting for him to let her out. They would go to parties and track down enemies and save entire species, all while the Ponds slept. He got to know River a lot better but she was always very secretive and she never let anything slip.
He thought River was beautiful. He had seen a lot of women in his nine hundred plus years but River was something special. He supposed to other people they might look odd together, her looking older than him, but it wasn't like that because they both knew who was older, and it was not the same person who wore the trousers in their relationship.
He sometimes wished his travelling in Time and Space would be simple. That he would be able to go around saving people and look at the great wonders of the universe without everything being so complicated. It always got complicated when he added companions to the mix. But he needed them, without them he made the wrong decisions, he didn't know what was right or wrong without a human there to teach him.
But sometimes he wished things could be simple.