It was like a blip, like a small light in the back of his mind. Stashed away to be remembered and recollected in an instant, but laying dormant so as to not interfere with normal functioning. But once that light faded, he noticed, and he gave a start.
The Doctor stared at the console before him, his hands tightly gripping two of the dividers as his eyes stared blankly at the glass column in the center. Its eerie blue light seemed calming, rationalizing his mind as he slowly accepted what that light meant.
She was gone.
It was a thing he knew would always happen – and, depending on when he was – was something that had already happened. But when there was a reason he counted his age in Earth years, and why he seemed to stay relatively on track with the Earth and its inhabitants. And they were good reasons.
He seemed to have a knack for picking up companions who came from the same Earth and who sometimes even banded together to help him and the world. And he seemed to have a knack for knowing of how to think of them.
The TARDIS was, after all, a time machine. She could go anywhere in time and be with whomever her occupants wanted to be with. The Doctor could easily go back and see her, be with her, just…relive those times.
But it never felt right to do so.
To say it was out of respect for the passed would be only half the truth. The hidden truth was the fact that he had a heart, he felt emotions, and to see her alive while knowing her true end was something that weighed heavy on his soul.
"Doctor…?" Amy's voice was quiet and gentle, knowing his silence and stillness were not out of perplexion but quiet grieving. "Is there…something wrong?"
The Time Lord glanced through the column towards the voice, his eyes resting on the carefully inquisitive faces of his current fellow travelers. Rory had his hand on Amy's shoulder, gripping it tightly as he exchanged a look that almost seemed to understand.
"Yes," the Doctor replied curtly, swallowing after. "In the sense of fairness, there is. But in the sense of the universe…no." He closed his eyes, stepping back from the console before sinking his face in his hands, sniffling as he dragged his fingers through his hair and sighed.
"You've…lost someone, haven't you?" Rory inquired, his tone defying the professional nature he had been trained with. Amy bolted her gaze at him, confused as to how he had drawn a conclusion so quickly. He shook his head. "It's…that look. You see it in the hospital when…"
The Doctor held up both his hands, eyes fixated on the reflection from the black pool through the glass floor. He rocked on his heels a few times before closing his eyes and lifting one of the hands to cover his brow.
He was allowed to cry. And thankfully, they understood.
"Everyone who enters this TARDIS, who comes with me, who sees the sights of the universe and gets to live that adventure they never thought possible…at least one thing of them is certain." The Doctor looked up at the two humans who stood opposite the console of him, their expressions calm but sympathetic, understanding in all the means. "They all will die, no matter how much I'd rather them not. It is…life, after all. It's simply the flow of time, the way it has to be."
"So do you know how…we'll die?" Amy gestured towards Rory and herself, her eyebrows raised and afraid of the question she had asked.
Hesitating, the Doctor curled in his lips, chewing on them for a brief moment, both to think and to stabilize his voice. "I know you will," he said finally. "But I don't know when and I don't know how."
"But you could know, right?" Rory's tone suggested he had a hard time believing the Time Lord hadn't taken a peek.
"I could," he answered on a breath, "But I don't."
Their eyes gave away that they wanted to ask why, but they instead remained silent. He chuckled, rubbing his nosebridge. "It's because anyone I call my friend is someone I respect. There is no cheating when it comes to respecting another. I have the best cheat sheet in the universe, and I could find and get all the answers if I wanted to. But if I were to do that, then there would be no point in existing."
"…That's not all of it," Amy murmured, prying for the full truth. "It isn't just that, come on Doctor."
He couldn't help but smile and laugh. Why were his companions so good at figuring out his layering technique?
"It's very simple," the Doctor said, sticking his hands in his pockets. "It's a factor of two. I respect you all and…I love you all too. So for me to look at you and see nothing but an end…it would make the adventure obsolete."
The married couple nodded, Rory hugging Amy's shoulders before the Doctor glanced up at the shining metal radials on the ceiling. They were bright, reflective of the multitude of lights and colors that composed the TARDIS, and the overall radiating appearance lifted his spirit.
The feeling still clung, his body aching the longer it settled in. It wasn't fair to her to be taken before what seemed right, before she had a chance to continue doing so much more. But what she had done was incredible.
Her life contained a track record most could only imagine accomplishing. Traveling the world and the stars, meeting creatures and races beyond the imagination, being in the action of what was thought to be the end...She had saved the world in ways that made him envious but proud. She had lived her life with unparalleled enthusiasm and energy, inquisitive of everything just a bit odd to cross her path. She had loved and been loved, probably in ways even she didn't know all of.
The Doctor kept on a certain track of Earth in order to stay on the same stream as those he had deemed his friends and allies. When they passed, he wanted to know – and experience that moment when he learned. It reminded him of life and how incredible it was, but also of the individuals that had enriched his own. It was something he never wanted to gloss over, for fear of growing distant and cold, and for want of being, well, somewhat human.
Sighing, the Doctor went back to the console, flicking a switch and punching in the new coordinates on the typewriter. The words unraveled on the screen and he smiled, sad but accepting.
"Good bye, my Sarah Jane," he murmured, closing his eyes as just one more tear rolled down his cheek.