It had gotten slightly colder.
He noticed it right after she was gone, after he had returned to the inside of the TARDIS. How the air became a bit more brisk, the various knobs and dials and buttons on the console all growing slightly chillier. While not a drastic change, he still had to tighten his tweed jacket around himself, River's efforts to distract him with mindless chatter just a distant buzz in his ear.
At first he wondered whether or not it was the lack of her presence- she did always have a special warmth around her- or if it was that somehow the TARDIS was grieving that caused the shift. He figured it was a combination of both. Without her constant light, her sly Scottish humor, the way her red hair always seemed to fan out a bit when she was frazzled, he was reminded of all of his friends, his friends that had left him (willingly or not), and that always made his heart feel a bit frozen. Or maybe the TARDIS had sensed the lack of raucous laughter in the middle of the night, the frantic energy that filled the console room immediately after they came back from an adventure. He knew that the TARDIS could feel the people and the atmosphere and was certain that the dimmer lights and the quieter whirrrrs and whooshs she made when traveling had something to do with it.
Even River noticed it, remarking on the decrease in temperature with her signature cat-like grin. He had merely offered a brief "hmm" in reply, choosing instead to sit down across from the controls and look at nothing. Noticing his response, she didn't say anything more and kept mostly to herself until they had arrived at their destination.
That was how things mostly went for the first few months, him drowning in his melancholy and River trying more and more desperately to pull him out of sorrows. He knew he might have been being a bit over-dramatic; he was certain he was probably coming off as rude. He tried his best to be as chipper as he normally was (or at least pretend he was), but without her by his side, he felt a certain emptiness, a consistent pang within his two hearts.
But it wasn't just sadness he felt. There was a certain…anger in him now. A dull throbbing at best, a burning rage at worst; a rage at the Weeping Angel for taking her, a rage at himself for letting them, a rage at the universe for just being so goddamned unfair. He now understood why people, his enemies, called him the Oncoming Storm; during those periods of fury, he felt a storm, a blazing tempest within his soul that made him question his morals (and self-control) on more than one occasion. It was the times when he was enraged that his eyes swam with red, that he felt his two hearts quicken with his angry thoughts. Those were the times when, reflecting on them later he would find, he truly scared himself.
While he harbored anger at a lot of things, the one thing he could not bring himself to hate was her. He couldn't find it in himself to think harshly of her actions; after all, she had only been acting out of desperation and her love for Rory.
A funny thing, love. He had seen civilizations built, conquered, and destroyed for it. He felt a special love for all his friends, gone or not. Yet, he knew he could never have that type of love, the kind that Rory and Amy so obviously had for each other. Now, that's not to say he'd never felt it before; he still occasionally thought of that remote beach in Norway and what had transpired there, feeling a gentle tugging on his heartstrings. However, he could never allow himself the joys of being in love, let alone a relationship; in the end, there would only be pain and heartbreak for the both of them.
And so it was, he was destined to live a life of loneliness. He would never admit to it out loud, not when he was constantly traveling with one of his brilliant, beautiful friends. But he knew they could tell; it was most likely written across his face, hidden in his eyes, weighing down upon his shoulders. It wasn't that he always needed to be around people, but more of the fact that if he wasn't, his mind would return to the dark, horrible place it had gone many a time right after the Time War.
He had come dangerously close to it after her disappearance. Luckily, River had been there, doing everything she could to distract him, even if it was clear he wasn't in the mood.
Sometimes he was thankful for the new found briskness of the TARDIS. When he found his mind drifting to the dark place, a mysterious breeze would pass by him, bringing him out of his miserable reverie with a shiver. Later, when he realized what had been happening, he would give a thousand silent thanks to the TARDIS.
It didn't take as long as he would've thought for the cold to disappear. He supposed that that was how grieving was sometimes; a long period of night and then one day, before you knew it, the sun was rising and a new day began.
He still wasn't completely healed from the ordeal. It was often the little things that would get to him. One day was particularly bad; it was mid-afternoon and it had just stopped raining. When he stepped outside to survey his surroundings, he was hit with an overwhelming smell of petrichor.
He spent the rest of the day locked in his room.
The day passed though, and time went on. There were hardly anymore incidents like that one. It wasn't long before the Doctor found himself in the console room, leaning idly against the railing, staring off into space. It was probably sometime around dawn, and he had been thinking about the swimming pool in the library and whether or not he should remove it (he would eventually decide the benefits greatly outweighed the risks) when he felt a warm breeze brush past his shoulders, gently heating up the surrounding atmosphere. Looking out the window, he saw the sun beginning to grace the horizon. A new day.
He gave a small smile and whispered his thanks.