There are spectacular days, days when The Doctor comes to call and no one dies. There are good days when The Doctor comes to call, and only a few are injured or die. Then there are bad days when many people die, or everyone dies. Those days are the worst. He can handle the others, but those days remind him of his past and all that he wants to run from. It during those days that he looks in to a mirror and sees the blood on his hands and no matter what he does, he hears the voices in his head. The faces of those he let down float before his eyes, whether they are open or closed. Nothing helps, nothing consoles him and the TARDIS tries her best to make him happy, placing fish fingers and custard in front of him because he is almost always happy when he sees and eats it.
Things are different now. It only adds to his pain, a pain so great that he feels as if he will burst and all he can do is let out an animalistic scream. The dish reminds him of something he lost, his Ponds. The TARDIS understands, but it is all she knows how to do other than fill his head with songs in a long dead language, which only adds to his pain, reminds him of a home he destroyed.
Nothing will console The Doctor and he cannot bear to pick another companion. He's far too old and they always leave and break his hearts. What will make the pain go away? Meditation does not help. The noise in his head grows too loud. All of the voices speak to him, asking "Why? Why? Why did you do this? How could you do this? Why didn't you save us?" It drives him insane, mad. He thinks about calling River, but she will never understand. At the same time, he cannot bear to bother her with his problems, not after how hurt she is over losing her parents.
The realization of being alone hits The Doctor like a ton of bricks. He stands at the console and cries. He moves to the chair and cries. Eventually he is in his hammock tinkering with the TARDIS, he has stopped crying, but his eyes are heavy with pain, loss, and loneliness. By this point, he has stopped talking to himself. It is at this point, he stops mistaking calling out the names of all of his companions, from Susan to Amy and Rory. He knows they are no longer with him. The Doctor knows he is alone and accepts it. The TARDIS no longer redirects phone calls, she doesn't even accept them. Together they drift off in to space, a lonely god and a magic blue box.