As promised, here is the reason this story is rated T.
Why should she be scared? She was the Mistress, after all. She could have whole galaxies falling at her feet in the course of a few hours. So why couldn't she face the Doctor now?
Quietly, she took a few steps closer, walking as gingerly as though the floor was ice, until she stood right beside the bed. Her tongue seemed to be stuck, because every time she tried to talk, no sound came out. Instead, she sat down on the bed, the little jolt causing the Doctor to open his eyes groggily, turning to look at her.
Once he saw who it was, his eyes snapped open properly. "Missy?" he asked worriedly. "What's wrong? Have we landed again?"
He began to sit up, but Missy put a reassuring hand on his shoulder to keep him in place. "No, that's all fine."
"Oh." He wasn't really sure what to say next, how to continue, as he had no idea why she was even there in the first place. "Did… you need something?" He shifted uncomfortably, realizing that he was in a rather compromising position.
Just say it! Missy screamed internally, while on the outside, she could barely get through a word without tripping up. Right now, all she found herself able to say was, "You win."
The Doctor's brow furrowed in confusion. "What?"
"You win," she repeated, gaining confidence now that she had finally begun her speech. "Your little friend was right. I don't have amnesia; I never did. It was all a trick, but… it didn't work. You win."
She expected the Doctor to be angry, maybe to chase her out of the TARDIS, back to her own. She expected him to run away from her, like he always did in the end, leaving her yet again to drift aimlessly through the universe, alone.
But she didn't expect him to smile up at her like a smug child. "Is that all?"
Missy stared at him in disbelief. Why wasn't he upset? She had tried to sabotage everything he believed in, and now he just laid there like a careless ten year old, as though none of this even remotely bothered him.
She wanted him to be angry. And not like before, not when it was just for fun. She didn't want him to be angry just for the sake of seeing him suffer; she wanted him to be angry because, right now, it was the only emotion that made sense. He should be angry with her. So if he wasn't, she'd just have to make him angry with her.
"I set that trap with the Daleks." Still, his expression didn't change. "I landed us in the graveyard." If anything, his smug smile was growing as she talked. "I took us to Clara." Nothing. Finally, she snapped. "Well, go on then, throw me out! Imprison me! Do something! I tried to trick you into giving up your moral code; KILL ME!"
For the first time since she had started talking, the Doctor's face twisted into anger. "Don't ever say that," he growled, sitting up, "because I've come very close. I've seen you die, and it's not something I want to think about ever again."
She felt a pang of guilt for even suggesting it. And for the Master, any form of guilt was rare. "Then be angry with me. Why are you so calm?"
"Because I already knew."
Missy froze, not sure if she should truly believe this. "What?"
"I knew you were faking," he shrugged.
"How?"
He scratched his head as he tried to recall the exact moment. "To be honest, I wasn't sure at first. I didn't trust you, and I knew it was probably a trick, but I couldn't be sure. Then, on that day when I tried to reach out to you telepathically, I saw your eyes. There's something in them—ambition, maybe—that's a dead giveaway. I knew you had to be lying."
He couldn't be serious. She had been so careful. Could she really have been thwarted by something as simple as that? "What about Clara, then? You told her you trusted me and not her."
"And I know you saw our conversation outside. You were at the scanner when I walked in. At that time, I explained that I knew you were faking, but I couldn't tell you that I knew, so you had to stay here."
"But why?" she asked, getting more and more frustrated by the second. "You could've just dropped me off in my TARDIS and flown away, like you always do. What makes this time so different?"
Her words were stinging, and the effect they had on the Doctor was obvious. His face fell, but instead of lowering his gaze, his eyes bore into hers, betraying everything he felt. "Is that what you think of me?" he whispered. "That I would just run away when you need me?"
"That's just it," she began. "If you knew that I was lying, then why would you think I need you? I don't have amnesia, remember?"
Now, he actually did avert his eyes, instead choosing to stare intently at his hands, which were fidgeting in his lap. "I don't know…" he sighed. "I just thought that… maybe there was a real reason you came here in the first place, that maybe you just needed the company. And I figured that as long as you were with me, I'd make sure you stayed out of any real trouble."
"Did you need the company?" The question was not asked in her usual tone; there was no intent to mock or joke or harm, and there was nothing venomous in its delivery. It was a simple, innocent question, and she stared at the Doctor with those wide, crystal blue eyes as she waited for an answer.
He thought of millions of different ways to reply to this, a million lies and a million half-truths, but when he came right down to it, there was only one answer that was completely true, no embellishment needed. So now he reached up one hand to gently cup the side of her head, as he said, "Yes."
The Doctor leaned forward to press a gentle kiss to her lips, but she replied hungrily, throwing her arms around his neck to draw him closer, closer. This took him by surprise, and for a moment, his arms flailed as he tried to recover. Finally, though, he responded, moving one hand to entangle in her hair, while the other wrapped around her waist, pulling her onto his lap. He opened his mouth to breathe in her sweet scent, the taste of Gallifrey, and he felt her tongue collide with his, causing him to pull her even closer.
At the same time, his mind reached out to hers, hoping to establish a connection, though he'd had no success in the past. But this time was different. This time, she opened the floodgates, and everything came rushing out, all her memories, emotions, thoughts. They all hit the Doctor at once, causing him to gasp.
And for a moment, he could only sit there, holding her in his arms, as he felt all the pain and anguish that she had faced, all that she'd suffered just to survive. He saw the insanity, the cruelty, the violence, displayed before him, and he couldn't help but feel sorry for her.
Maybe they weren't so different, after all. He was just as broken, just as lonely. But he would occasionally find people who would help him forget all of that, at least for a little while. Missy, on the other hand, had no one. No one but him. And he so callously flew away every time she needed him, because violence was the best way she knew to get his attention, and it inevitably followed in her wake.
He brought his lips to hers more softly now, an act of love to show her that he was sorry for all those times he had left her behind, all those times she had felt abandoned. He trailed gentle kisses down her neck, pushing off her jacket so that he could reach her collarbone, to skim his tongue along her soft, smooth skin.
When she felt his teeth start to dig in, she let out a gasp, and he smiled, sitting up to face her now. "I think you might need to change your name after this," he joked. "Not really the 'Master' anymore, are you?"
"Shut up," she said, pulling him roughly into another kiss.
When the Doctor found that he was finally able to speak again, he continued. "But you'll always be my Koschei."
"My Thete," she smiled deviously as they fell back into the bed.