Disclaimer: I don't own it. If I did, the Daleks wouldn't come in designer colors.
She found him in the library. Just sitting. He wasn't pretending to read like usual, didn't turn in Amy's direction when she entered the room. She knew he had heard her walk in but she was unsure of what to say. He didn't acknowledge her presence. Of course he noticed, but what was he to say? In the worlds that spun inside his mind, he was so utterly alone. Amy had caught him in a moment when it was unbearable to think, to move, to even see, in a moment when he could feel the universe and was too afraid to let go. The Doctor was cursed, like all Time Lords, with seeing of how little consequence he was in the scheme of things, and when there was a pause like this in his running and laughing and saving, it was all he could do not to let it engulf him. In this new body, younger and older than ever before, it was all the more obvious that he could only save a few, and that someday he would cease to do even that.
Amy sat down next to him and tucked her feet up, still saying nothing. It was probably best not to bother him, she thought, but all the same it was impossible for the small child inside Amy to leave her Raggedy Doctor alone. She laid her head on his shoulder and closed her eyes, focusing on the most peaceful, languid thoughts in her head. The two of them watching the sunset in Space Florida, the calmness of the silence of space when a star was forming. She knew he could, to some extent, pick up on her thoughts, so Amy grasped the Doctor's hand and told him mentally that everything would be alright. It took some minutes, but when he squeezed her hand tightly back, she knew he was coming back to her. The Doctor seized onto Amy's memories, and while he still sat in utter sadness and despair, the gentle pressure of her head on his shoulder made all the pain a bit more tolerable.