“And now all is quiet aside from the grind of the engines. The TARDIS has never seemed so big and empty. The Doctor steadies himself against the desk as the loss of Amy crashes into him like a wave. A sob is getting through. He looks so old, so sad and so alone.”

Steven Moffat reads aloud stage direction from the end of The God Complex

The Doctor is the most heartbreaking character on TV. He knows he either has to be alone, or destroy someone else’s life. He knows it’s selfish to bring people along with him, but the alternative is so much worse. We saw Ten after Donna left and he decided to travel alone. It’s not good for him. So his choices are basically do what is best for him, or do what is best for others. As much as saving Amy and Rory was the right thing to do, I can’t see the Doctor leaving it there. He is too lonely, and too involved in their lives now. There cannot be a clean break.