Later, after the events in Mercy, Amy asked the Doctor about the Master. She had heard bits and pieces, and had previously assumed him to be some lunatic mastermind who the Doctor had battled in his past. Of course, he still was a lunatic mastermind. But there had been something in the Doctor’s face when he had mentioned him in Mercy, something that made her wonder if there was more to what they had been.
“We grew up together, and it went wrong.”
That was the only thing he would say, and he promptly abandoned the conversation to become very interested in a gear under the TARDIS console.
“I told you how he was mad, Amy. That was why it went wrong.” The Doctor’s voice was terse, and Amy wondered if she should not have asked. The Doctor was unstable enough as it was, lately, and the Master was obviously a touchy subject. She couldn’t get rid of her curiosity, however, so she still wondered.
“Access records: The Master.” Amy pulled up the TARDIS’s information about the Master when she had a moment alone, and read about what he had done throughout the years, going backwards in the Doctor’s timestream. She started with the year that never was, horrified, and quickly skipped through that. As she went backward, however, she noticed a pattern.
Even though the Master did horrible things, and hurt many people in the process, his escapades were always immense spectacles that attracted the Doctor every time. Amy was almost amused, because it seemed like what the Master did was merely to get the Doctor’s attention. It was as if their interactions were an immense, complex game. The Master’s actions seemed like conquest on the outside, but as Amy read further, that seemed to be only a facade. The Master’s actions seemed to be for the Doctor, and only for him.
“Oh good lord, I bet they were shagging,” Amy murmured to herself, not sure whether to giggle or recoil. “Have to wonder what River would think, if he ever came back.”
The Master appeared to have died, after the events of Gallifrey’s attempted return. Or at least, he had disappeared, so Amy didn’t think that any of them would see him any time soon, River included. The Doctor had mentioned him along with the Daleks, however, and they always came back. So Amy had to wonder if she’d see this strange foil to the Doctor during her travels.
“Amy, what are you doing?” The Doctor’s voice broke her out of her reverie, and she shut down the Master’s data file, turning around and giving the Doctor an innocent smile.
“Just perusing the archives,” Amy said vaguely, but the Doctor gave her a look.
“That is what I was doing, Doctor.” Amy’s smile vanished. “I have a right to read the archives to learn things.”
“…for the record, whether we were shagging or not is none of your business - “
“I can wonder what I like, Doctor! You sleep with my daughter!”
“Who’s shagging?” Rory came into the console room, looking bewildered.
“No one is shagging!” The Doctor flailed his arms, and Amy burst out laughing.
“Just talking about the Doctor’s ex-boyfriend - ” Amy began.
“Amelia Pond, no one ever said anything about an ex-boyfriend!”
“…yeah. I’ll leave you to it, then.” Rory stifled a laugh and wandered back to his and Amy’s room in the TARDIS. Amy folded her arms and stared the Doctor down after Rory left.
“Unless you say otherwise, the Master was some sort of ex of yours in my mind,” Amy said, and the Doctor sighed.
“It’s in the past now, Amy. It’s irrelevant.” There was a note of sadness in the Doctor’s voice, and Amy began to feel a little guilty for teasing him. She put a hand on his shoulder.
“He’ll be back, Doctor. He always comes back,” Amy offered, finding that she was extraordinarily bad at comforting.
“Yeah. That’s what I worry about,” the Doctor muttered, but Amy couldn’t help but notice a hint of glee in the Doctor’s voice, at the idea of the Master coming back.
Yep. They had most certainly been shagging.