The Doctor didn't return to the Tardis until hours after Missy stormed out of Me's house, he hadn't known how to approach her after the obvious hurt he had caused. And he didn't bother checking the tracker she was wearing either, knowing that he would find her exactly where she had said she would be, once he got up the courage to actually go looking.
For the first time ever, when the Doctor walked into the Tardis it felt wrong, as though he was an intruder.
Sighing regretfully, he laid his hand on the console, which seemed to vibrate angrily under his fingers. "I know, I made a mistake."
If a time machine could roll its eyes, the Doctor knew that's what she would be doing, not only because he hurt his friend, but because of his short sightedness of what could happen if he pushed too far for answers on something he had deliberately forgotten for a reason.
"Missy was right, and so are you, this is something I need to leave alone, at least for now." He told her quietly, running his fingers gently across the surface. "Now I know you're probably helping her hide, but I need to speak to her, so will you help me old girl? I promise I'll make this right."
The gut instinct that he needed to go down to the engines swept over him and he smiled in thanks, before quickly hurrying off down the corridor.
He lightened his footsteps as he got closer and carefully shielded his mind, not wanting her to sense him and run before he got the chance to talk to her.
Rounding the corner to the section the Tardis had pointed him to he stopped warily, unable to see the Time Lady.
After a moment, he heard a clang and a heavy Scottish accent cursing angrily as Missy slid out from underneath a computer panel, a layer of grease clinging to her arms and clothing, with another smear across her cheek.
At some point since she had gotten back, she had changed into a pair of dark purple trousers and a long blue shirt that had the cuffs rolled back to the elbows. Her hair had been brushed out and then tied back into a simple pony tail to keep it off her face.
"If you want me to fix this so badly then the least you could do is stop electrocuting me." She told the Tardis, hands on hips, a fond smile creeping onto her face as the screen just flashed at her noncommittedly.
Coughing slightly, he took a step closer, "Missy?"
The smile disappeared, and she turned away, seemingly about to leave.
Darting forwards he caught her wrist, "Missy wait, please."
Pulling free, she turned back around, staring at him for what felt like forever, before eventually lying back down and sliding herself back underneath the panel.
"I need to borrow your screwdriver." She demanded, holding out her hand expectantly until he dropped the sonic into it.
As the buzzing began whilst she continued working, he sat down with his back against the panel.
"I'm sorry." He told her eventually.
"It's fine." Came the reply, sounding cold and unfeeling.
The Doctor just sighed, "No, no it's not. You were right, I'm a hypocrite, and you were right to do what you did. And I knew it was wrong as I was saying the things I did, I just didn't know how to stop."
The sonic stopped its buzzing and then suddenly she was back out and sitting in front of him. "Do you think I don't understand it?" She asked wryly, "It's taken the last eighty years for me to really start trusting you again. You've only really had the last week to start believing that I am trustworthy in return. I get it, but that doesn't change how much it hurts." Missy told him hesitantly, choosing her words carefully.
"Things used to be so much easier between the two of us." The Doctor muttered, frustration ringing in his voice. "What happened?"
"I went insane, you ran away, I tried to kill you, you tried to kill me. We have spent most of our lives since we left Gallifrey, locked in a constant cycle of being at each other's throats." She told him, twisting so they were sat side by side, staring at the Tardis wall in front of them, which was pulsing slightly.
There was a long silence that stretched out between them until the Doctor finally gave his whispered confession.
"I don't know what we are without that."
Missy just shook her head helplessly, "I don't either."
"So, what do we do now?" He asked her tiredly.
"I want to be your friend again, that was true. And I know it's a lot to ask and it's going to be hard, but I need you to trust me, trust that I'm not going to hurt you. Just that. No matter what else I do wrong, no matter where else I fall, I need you to trust that you are the one person I will never hurt again." Missy told him seriously.
With a small smile, the Doctor turned his head so their eyes met, "I can promise to try, I may misstep but I will never forget what happened today. I am so sorry Koschei."
Leaning her head against his shoulder, she hummed contently, "Then I forgive you, but be warned Theta, if you do it again I won't just walk away, I'm probably going to slap you."
"If I do it again, I'll probably let you." He chuckled.
He felt tugging at the edges of his mental shields and let them fall away as she reached out for his mind, there were parts of her memories still locked off to him, but he no longer begrudged that, knowing she was doing it for the right reasons and not to spite him.
With the return of their psychic connection, he could see just how much their argument had hurt her which made him wince slightly, but he could also see how honest and genuine her desire for him to trust her was.
He relished in that feeling of certainty, appreciating just how open Missy was being, even for a species with the ability for telepathy, Time Lord's usually held a lot of themselves back, but almost anything he could want from Missy's mind she offered freely. The only exception being those few short, in terms of their life spans, memories which had carefully been tucked away.
"So, have you been down here the entire time since you got back?" The Doctor asked her curiously, having not realised she had still been doing repairs to the Tardis after telling him that the list of priority repairs was completed.
Nodding slightly, she gestured around the room, "This entire section needed rewiring and there were some parts that needed replacing entirely, but luckily you have some long-forgotten storerooms hidden away that I raided earlier. The panel here is still glitching and giving false readouts, which is what I was working on when you arrived."
"No wonder the Tardis was so angry at me when I came in, she must be worried I'm going to make you want to leave before you finish fixing her up." He laughed.
Missy chuckled, holding out her hands so he could see the minor marks from the electrical burns she had received, "Well if you could ask her to stop zapping me that would be much appreciated."
Running her fingers over her palm in sympathy, he tugged at the edge of the shirt she was wearing, "A little modern for you this, isn't it Missy, or is the Mary Poppins look finally becoming dated."
"Never." She told him gleefully, "But I am not wearing a corset to go crawling around the inner workings off a Tardis, especially if no one's around to appreciate the grace and posture that would require."
"Well I must admit, I quite like it." He told her lightly, "It makes you look more relaxed and at ease."
Humming in the back of her throat, she just pressed closer against his side, shushing him when he tried to speak.
So they just sat there in a comfortable silence until Nardole came to find them hours later, enjoying the calming presence of each other's company.