The Doctor knew better, at his age, than to have expectations as to how the universe worked. At the same time, he knew that this wasn't how it worked.
Amy could only fix that which she knew about, and whatever the logical explanation for her bringing Rory back was, it could only happen once. There wasn't anyone else she cared about to bring back even if the Doctor had been banking on her caring about him he hadn't really dared to hope.
All that considered, the Doctor couldn't say he was completely surprised when time unravelled and was knit together, and he opened his eyes to see the Master.
The Master hardly took the change in his stride, though. "What?" He was, curiously enough, in the same incarnation that he had been in before, down to the grin, even if it was more uncertain than it had been. He shot the Doctor a look, before continuing. "You are the Doctor?"
The Doctor nodded, a little surprised that there would ever be any doubt. "Younger and prettier, but still me."
The Master reached out a hand towards the Doctor, before snatching it back. "You're very different. More here." Another pause, then he continued, wondering. "I can't hear the drums anymore."
"Yeah?" the Doctor asked, as conversationally as he could manage. He had no idea what was going on, there was no way he could think of to explain what was happening, but it was always important with the Master to seem like he was in control.
"So you're not the only one who's improved."
The Doctor couldn't keep himself from cocking an eyebrow. "You think I'm improved?"
The Master licked his lips as his eyes carefully trailed across the Doctor's form. "Definitely improved."
The Doctor laughed, delighted.
The hand that the Master extended this time stayed out, reaching forward gradually towards the Doctor's face. The Doctor moved his head forward, since he needed that physical proof of existence every bit as much as the Master did. They connect and it's a little like when two instances of the same minor object touch, apart from the fact that their connection never used to be based on similarities.
The Doctor couldn't say that he was surprised when the Master slid his hand around to the back of the Doctor's head and used it to draw them into a kiss that was neither harsh and biting nor gentle and studied, it just was.
"You willed me back into existence," the Master accused when they'd separated. Even if the Doctor had only intended it to be a brief separation the Master had always had the habit of relying on words whenever he could.
"I did," the Doctor said, because he'd figured out by now that there was no other way that this could have worked.
"You willed me back into existence right," and it seemed to matter to the Master how the Doctor responded.
"You were never supposed to be mad," he said after a pause that the Doctor knew had made it clear how much he was struggling.
"No, that was always my choice."
The Doctor didn't know if that was meant to be a thank you or an apology, but that was the thing about the Master. He was never meant to understand when in the other Timelord's presence, just to react.
There was really only one thing the Doctor could think of to do when the Master looked at him that way, so he surged forward, resuming their kiss.