This is part of my "Stay with Me, I Need Support" series that has a somewhat-reformed Master traveling with Eleven, Amy, and Rory, with visits from others. "They Have Been There from the Start" is a sequel to "I Can Only Dream in Red". Not my characters.
Your relationship with the Doctor is a difficult one, filled with pain and doubt, where every time you see him he knows less and less about you. But it is not nearly as difficult as the relationship the Doctor has with the other last Time Lord, the one he has instructed her never to mention next time she sees him for fear of paradox, the one calling himself the Master.
Your instinct is to hate the Master for all those centuries he had with this wonderful man, and even more so what he did with them, his use and abuse – except the Doctor as you know him would never be this way without him. So you owe him as many thanks as you do insults. The Master is not as he was then, either. He is like a poisonous, sharp-thorned tree that has been trimmed into a bonsai, still prickly but something the Doctor can keep in his TARDIS with minimal fear of injury. You tread lightly. He cuts, but is cut so deep himself you must cultivate as you prune.
You're glad that Rory and Amy are aboard. The two Gallifreyans would feed on each other into madness left alone too long, and sometimes even the Ponds are not enough, though they make your stay have elements of comfort and fun rather than just desperate affection. That's why Amy called you. That's why you're here: payment on the installment plan for a necessary crime not yet committed (wibbly wobbly).
You don't let the Doctor know that this is not the first time – spoilers – but you can see it is for him with you. And what of you has he seen? How much can he trust? What does he know? He babbles about rarely interacting in this way with humans, and that so mostly out of loneliness once in a green sentient triple-moon, but you brush his hair back and kiss his cheek and he calms.
It breaks you, it really does, that the Doctor so much needs his opposite to capture and torment him, even in the relatively harmless, symbolic way they do now, and that the Master in turn switches back to the wilder darkness that shows what he must have been like in the old days before.
He curses and jeers at the Doctor as he straps him to a table, shackling him immovably, the Doctor meekly submitting with only perfunctory struggle. It is only the knowledge that blindfolded, gagged, helpless and hurting, that these are the only times the Doctor can truly let go of his responsibility, the running hamster wheels of his mind, his public guilt and private shames, only this brings you to play along in the this twisted tableau.
Amy (much less Rory) could never restrain themselves to the role you've been asked to play. You can. The Doctor doesn't always require what you can provide, but when he does it is vital to his very sanity.
In 21st Century parlance, you are there to be The Good Cop. The Master prods, shocks, beats, pierces, burns, freezes, slaps. He yanks and hits. He kicks and screams. You caress and soothe. You provide water and warmth when timidly asked. You let him hear you ritually reprimand The Bad Cop when he goes a centimeter too far in harshness. You tell him he's beautiful (which is gloriously true, even enhanced when he's slick with sweat and other things, panting and gasping), that you love him more than anything (painfully true), and you promise everything will be fine (which is one of your sweeter lies).
You make it possible for him to speak, hold his hand and stroke his brow, as – at his prior request, though it looks torturous – the Doctor is brutally taken by his friend-enemy-lover.
Oh sweetie, it will get better.
Does he…love me? Will – umh - he ever?
I love you. Is that enough?
When the Master is finished, you let the Doctor loose and hold him for a while. Then he crawls, naked and afterglowing, to a better position and thanks you with clever fingers and tongue (and oh, it's far better than it has a right to be).
It's not a happy thing. But it's a needed thing. And for now, that's good enough.