Dimly, he noted that this was reminiscent of losing Rose, but worse, if such a thing were possible. He only distantly was aware of Madame Vastra talking to him, and he felt sort of bad, but he thought, she's used to this by now, him not talking.
The loss of Amy had visibly affected the Doctor, noticeable immediately upon sight. His once bright eyes, alight with curiosity and joy, had dimmed, leaving his sunken face even more pronounced. His skin was far paler than what was healthy, and his hands shook harshly with every attempted movement.
Jenny, Strax, and Madame Vastra were now used to him either answering their attempts at conversation with something completely off topic, or rather, not at all, and as they had taken up a semi-permanent residence in his TARDIS, this happened quite a lot. He was used to their different expressions when they looked at him now, Jenny's worried, and Madame Vastra's deeply sorrowful. Strax had accepted early on that he was not apt to dealing with emotions, and instead insisted he stay to "protect his companions with the fierce threat of the Sontaran Empire."
So that was how his days went, a darker hue of grey every moment. His nightly routine however, and taken a path not visited since the early days following the Time War.
At some point, Madame Vastra would gently remind him that it was nighttime, and that he should get some rest, and he would begin his shuffle towards not his bedroom, but to his library. As he didn't pay a lot of attention to where he would walk, the TARDIS would have to gently lead him toward it, ensuring he got there safe and sound.
Upon arrival, he would sink into his chair at the centre of the library, and the TARDIS would softly sing him to sleep in Gallifreyan, sweet lullabies, sung to the infants on his home planet to soothe their mind and let then sleep. He realized early on that this was the only way he could get to sleep without being terrorized by nightmares, and waking up sweating and screaming, reaching out to hold a hand that would never again reach back. Though the lullabies helped, he never could sleep the whole night, and would eventually get up and walk to the console room, opening the TARDIS doors, and staring into space. He would then sit at the edge with his legs dangling over, until he would hear one of the TARDIS inhabitants awake, and he would get up, close the doors, and sit by the console, beginning again the routine that was now his life.
Except one night, with the Doctor lost in his thoughts, staring into space, Madame Vastra awoke early, and quietly made her way to the console room, to await the Doctor. However, seeing him already there, she decided to leave him alone. But as she began to make her way back, she stopped on her tracks and felt her heart break as she heard him murmur a plea into the darkness. She heard him sigh, and get to stand by the console, absentmindedly stroking it. She began to walk back to her and Jenny's room with his words echoing in her head.
"Please come home Pond. I miss you."