There was a story, a long time ago, some time ago, a short time ago, now, and it began like that:

The Doctor, the Captain and the Companion sat together, in silence, having eaten all of their chips, or at least, seemingly so. The Captain was watching the Doctor with steady eyes, all the time looking as if he were on the verge of asking a question. The Doctor was staring right back at him, warning clear in his posture, and that was it. They hadn't moved in the last ten minutes.
But because the story didn't end there (anywhere), eventually the Companion cleared her throat.
"I'm just gonna go grab some more food and some canned coke, ok?"
If they even heard her, they didn't show it, but after a few seconds of silence the Doctor's tense muscles relaxed.

"Go on, then," he said to the Captain. "I can see you are dying to ask."

"Will it change the answer?"

"No, but... Ask nevertheless."

"Who is the Master?"

"A friend, at first."

"Here it is. The Companion... She is brilliant, isn't she? You only take the best, after all. But she's young, still naïve, she can't understand that." He stopped talking and stood up, shook his head. "It's not such a bad thing, after all. I rather hope she'd stay that way, but we both know that is not possible," and there was sadness in his voice now, before he smiled again, self-deprecating and wry. "The feelings, the history, the longing in your voice... He wasn't just a friend."

The Doctor smiled sadly, but didn't correct him.

"You thought him dead, and mourned - oh, I saw you with the Bad Wolf, you danced with her and tried not to cry - then he somehow got back, and you both knew and both were afraid."

Still silence. The Captain decided to go further. He had to be sure - for the Doctor's sake as much as his own.

"The way you look at him, if only on a screen. The way you said 'Wife'. And there's him, of course, for how quick Yana was to trust you? His voice shake, when you named him, and he did kiss that woman, but he didn't look at her. And he wasn't ironic at all, asking for a - the Doctor. Was he?"

There was an unreadable expression on the Doctor's face and he wasn't there with the Captain at all. He was on Gallifrey, running with the Friend (best of them, only him, even if uneducated yet – him, just him, always him) through the red grass, their fingers entwined. Forever together, they'd believed. They might even have had a chance of that. He didn't dwell on why they didn't take such an offer, freely given. No. He was a Time Lord, and what was a part of his personal past remained so, he knew it. There was no point in dwelling... Or so he told himself.

'Then he somehow got back', the Captain had said not a minute ago, the Doctor realised suddenly, and it was more of a confirmation than seeing him with his own eyes could have ever been.

"You loved each other, didn't you?" the Captain asked now.

The Doctor looked up.

"Yes, Captain," he said slowly. "That I did. Do."

And because it was the end of the story (not really), the Companion came back with food, and they smiled and ate and congratulated her on a successfully accomplished quest for food, and all was as it had been.

And if the Captain, knowing what he did know then, objected to them staying together, and didn't kill the Master himself, but neither did he disarm the Bad Wife at the right time, well, that was altogether another story (or was it?).