Author's Notes:
I will say again, I like Jo Martin's portrayal of the Doctor, but there seemed to me to be a few characterisation inconsistencies, and this was written before The Flux. At the risk of spoiling my own work, of course she isn't a villain. She's the Doctor, but this was me patching together some issues that I couldn't get around.

Summary: The Doctor discovers who the true enemy is.

Two days later though and she’s no closer to finding him than she has been for the last several weeks. She’d become accustomed to the morose desperation of a seemingly fruitless search; she'd been looking for him virtually since she’d left the ruins of Gallifrey. She used to go back, just to look at the burnt out, blasted, forever-barren citadel, to walk in the dust that is all that is left of her hoped for redemption. She doesn’t know why.

Yes, she does.

Punishment. She should have been there. Or should have stopped him. Or should never have brought them back at all, should have let them die in the Time War, at least that had been for a greater purpose than the Master’s childish spite.

She’s never found any trace of the Master, though she’s certain he must have escaped the explosion. He has a talent for escaping such things. She isn’t having any more luck today, and today her inability is infuriating her. There’s a rage pulsing through her, not the white cold anger of her twelfth self, or the blank depthless fury of her eleventh. This rage is burning, hot as a newborn star, and capable of annihilating solar systems. Like this, she feels merciless, a vengeful god: powerful as a tornado, a tsunami, an oncoming storm. This rage could end worlds, has done.

She hates this feeling, it’s destructive and untidy and not helpful, but she can’t purge it, can’t fight it, because she’s trapped here in a cycle of desperation for some answers and an inability to find what she’s looking for.

In practical terms, this means that she’s been crashing and banging around the console for hours. The fam have long since gotten tired of her snarling at them and cleared off somewhere else. She’s grateful really, they don’t deserve her in this mood, but they don’t understand. They don’t understand that the Master had been her best friend and that she had loved him and thought the world of him and that every unpleasant and evil action is a betrayal. They don’t understand that even as her arch enemy, he has hurt her friends in front of her, used them as bait to lure her in, but never acted with this kind of sadism. Finding Jack when she had was pure chance. This had been nothing but sport.

They don’t understand that, since he has destroyed their planet once more, and forced her to do the same, they are the only two (and there’s that other one, but she can’t even think about that and about her, too complicated, too much). They don’t understand that that makes him her responsibility, her burden. His actions are her fault. Bad enough if he had done this to just anyone, but Jack makes it personal. This has happened to Jack because of her.

The fam doesn't understand, and they don’t deserve her temper, but she can no more control it than she could turn back a tide, control a storm. Their questions like the irritating questions of a restless child. She hopes they’re enjoying whatever they’ve found to entertain them. There’s the movie room and the swimming pool and the rainforest and she’s sure there’s a bowling alley somewhere. The TARDIS will find something for them.

Even the TARDIS isn’t speaking to her. Tired of having her buttons hammered unnecessarily and her levers yanked about, tired of being called useless for not turning up anything the Doctor can track on the scanners, tired of being blasted with silent rage. The emptiness of the usual comforting hum leaves a psychic blank, not painful, but unignorable, like the gap where a tooth should be that you can’t help sticking your tongue in. That frustrates her too.

Jack is mere feet away. Ryan and Yaz had brought up a chair and he’s sitting in it, head angled towards her. His hand white knuckled around the pole of the IV she had been forced to set up. He still won’t let her touch the lazer thread, and he can’t die. She has to get liquids into him somehow. He flinches at every crash, it does nothing but make her frustration ramp higher. She’d almost ripped the dematerialisation circuit right off the board when she’d seen him angle his face up towards the others in mute appeal when they’d been leaving the room. They hadn’t noticed, and she’s glad for that. It makes something low crawl in her belly that he’s afraid of her.

It grows claws at the knowledge that her clattering isn’t helping, but she can’t stop. Nothing she does helps the rage pulsing hot and bright behind the eyes, the drums the Master talks of, a throb with each beat of each heart, telling her that she must find him. Must find him now.

Another scan, across another timeline and another negative beep. The Doctor closes her eyes and takes a long, slow breath. He must be somewhere. “Universe, provide for me,” she growls out, a prayer or a plea, and turns another couple of dials. Still nothing. She bangs a hand down flat on the dashboard. “Stop sulking and help me,” she orders, a demand this time, and doesn’t look at Jack, pressed back in his seat as though braced for impact.

The TARDIS grudgingly materialises a few centuries back and a galaxy over, lets her scan and then flings them back into the void. She’s honestly desperate enough to chance crossing her own timestream if something doesn’t show up soon. He’d been captured by Nazis in 1943, perhaps she could just show up later that year. The TARDIS hums warningly as she plays around with coordinates, and with very bad grace she pulls her hands off the console. Not yet, then. She doesn’t kick one of the circuitry panels, but she thinks about it and hopes the TARDIS hears her.

Ryan enters, crashing through the door as he always does. His excitement and enthusiasm usually bring the Doctor joy, but today she’s turning to snap at him even before he stumbles over his own too big feet, catches a hand around Jack’s IV and goes down, wrenching it to the side as he does. The Doctor lurches towards them, but she’s on the wrong side of the console and she can’t stop the whole thing sliding a metre to the right.

Jack jerks with it, a pained cry leaving him and the now familiar duck of the head, as though he fears a blow for making the sound.

“Ryan!” she barks and her rage comes to the fore, burning yellow and sparking and ready to unleash on this new target. He’s self conscious about his clumsiness and she would never normally berate him for it, but even knowing all of that, she knows she’s going to shout at him, going to thunder with rage. She stomps across the console room, stamping her boots just to rid herself of tension. “Ryan!” she says again, louder this time, with a definite edge. The voice that had once told Susan that she really was serious and to go to bed right now.

Ryan has managed to stagger to his feet, so has Jack. As the Doctor takes the last couple of paces bringing her near enough to grab the IV to push it back into Jack’s hand, she watches as Jack gropes out with his other arm. For a second she thinks he’s doing the mute appeal he does, the one that makes her forget that she’s a pacifist and very seriously think about using the device still wired into Jack’s brain on the Master instead.

It’s worse.

He flails for a moment until he finds Ryan’s sleeve, then he grabs him and pulls. He pulls Ryan out of the way of the Doctor and behind him, stepping in front, as though he’s going to meet the Oncoming Storm blind and mute and still favouring his left ribs. As though he should ever need to.

It’s like a plug being pulled, or a power cut. The rage doesn’t drain out of her; it just disappears, washed away in one blank burst of horror.

“Hey,” Ryan is patting ineffectively at Jack’s shoulder. “It’s just the Doctor, it’s alright.”

Shame replaces rage. She wasn’t going to touch Ryan, of course she wasn’t, that had never even crossed her mind, but she would have hurt him.

“Jack, I wouldn’t…” she hears the cracks creep into her voice, knows she sounds raw and vulnerable: like Amy telling him that the other world had to be the real one because a world without Rory was impossible; like Nyssa asking about her father and if he was still alive; like Jo sobbing in his arms. “Do you really think I would hurt him? Hurt either of you?”

She’s been hurting the TARDIS for days, pummeling her, punishing her, like a spoiled child denied a treat.

Ryan pulls out of Jack’s grasp, reassurances falling off his tongue. Jack hunches into himself like he fears retribution. Jack Harkness never used to fear: Jack Harkness had laughed in the face of death and daleks. She doesn’t approve of the quick way he resorts to weaponry, but he is good and brave and, more than the damage wrought to his body, she is enraged by the damage done to his soul.

She forces herself to relax, to speak softly and evenly. “I am going to find who did this to you, Jack. I promise I am going to find him and make him sorry.” That’s true, even if she hasn’t quite figured out the how. The lights flicker in the glowing columns, TARDIS approval, and the Doctor smiles. “But I need you to understand that it’s me, that it’s the Doctor, and I’ll look after you, ok?”

Jack nods, a pre-programmed response. She hasn’t changed anything in his mind. She wishes his face wasn’t forced into that grotesque smile, that she could read something of his emotions.

“Wouldn’t it be easier if you could speak?” Ryan asks, echoing her thought. “The Doctor knows how to free your mouth up now.”

She doesn’t even think it will hurt that much, but he’s been subjected to so much, she won’t do that until he is ready.

For an instant, something of the old Jack is in his stance, in the tilt of his head. He can’t set his mouth the way he usually does, in that arrogant, determined scowl, but she can see he wants to. Her stomach drops. He thinks she wants him to beg.

“You don’t even have to ask, Jack,” she reassures. “I won’t do it, I know you don’t trust me, Ryan can manage, or you can do it alone.”

Something like hope suffuses him and she watches him tamp it down. He nods once, slowly, and she knows he thinks she is going to laugh in his face and refuse him.

“You? Or Ryan?”

There’s another silence, then Jack reaches up and tentatively taps Ryan’s arm.

She pulls the sonic out of her pocket and selects the correct setting, handing it to Ryan. “It’s being powered by your body heat,” she explains quietly, speaking to Jack, but eyes on Ryan to include him as well. “If we can cool it down, it should just turn off and then we’ll remove the control circuit. It might spark a little, but it shouldn’t read this as an escape attempt, so it won’t be that bad. As soon as it disappears, open your mouth as wide as possible, that’ll break the link.”

Both men nod.

“Ryan, you need to turn it on and then very carefully place it against the thread, don’t touch his skin at all. It’s going to get cold.”

Gingerly, Ryan does as she says, the familiar whir of the sonic begins. As the Doctor watches, the thread pulses a couple of times and Jack’s hands clench spasmodically. She wonders what he’s thinking, if he believes she is trying to help or if he thinks this is another torture being inflicted on him that he is being tricked into standing still for.

There’s another spark and he groans low in his chest.

“Just another second, mate,” Ryan reassures him, though the Doctor can see the worry in his eyes.

She steps up close and Jack must sense her because he snaps his head back and away. Luckily, at that moment the thread winks off and disappears.

“Jack, now!” she says sharply and a dozen memories from lives past flash across her mind.

Jack responds as instantly and as instinctively as always. His mouth opens wide and he reaches in with a finger, pulling out the curved metal something that had been forcing his lips into that hellish grin. He drops it to the floor where it sits, sticky with gobs of saliva and blood. “Thank you,” he rasps out.

She ignores him.

“Is that it?” Ryan asks, “Is that the on switch?”

The Doctor reaches down and picks it up and brings it to eye level. “No. This is something else. Jack, there must be another bit in your mouth.”

Fingers are already groping inside, but now he removes them. “It’s...it’s in my throat. Can I-” he stops, flinches, straightens, tries again, “Am I only allowed to remove the pieces in my mouth, ma’am?”

He’s always called her sir when he’s looking for direction, military mindset. John and Mike had both used to do the same. This isn’t at all like that.

“Can you do it without hurting yourself?”

He nods slowly.

“Then get it out.”

She should probably have made him wash his hands, but too late now. Mouth still open wide, preventing the lazer thread from reinitializing, he sinks his index and middle digit down his own trachea and gropes around. There’s a really terrible joke about Jack’s unsurprising lack of a gag reflex that now is not the time for rattling around inside her skull, then he pulls out a flat square about the size of a postage stamp and tosses it to the floor.

The Doctor recognises it as the control circuit, she’s been gagged with almost every piece of technology in the universe at one time or another. She doesn’t even bother to pick it up, just brings her boot heel down on it, shattering it completely.

Jack is stretching his jaw and massaging tattered lips. “Thank you,” he says again, more reverently this time.

“Don’t. Just don’t. I don’t deserve your thanks, I should have come sooner.”

“You didn’t know?” Jack sounds like he’s trying the words out for the first time.

“I didn’t know he had you, but I knew he was back. I should have thought-”

“She.”

“What?” Not Missy. Surely not Missy. Missy had been mad and capricious and spiteful but not monstrous, not capable of this.

“She. Not he.”

She thinks about Clara locked in a dalek casing and handed over for the Doctor to destroy. She would have thought Missy too fastidious to get her hands dirty in this way, but it’s possible she might consider getting revenge on Jack to be more worthwhile, more personal. Jack had seen him defeated and cuffed; had helped. And then there’s the nausea and the migraines that Time Lords get just from being around him, a fixed point, a wall that time itself slams into.

She shakes her head. “I’m sorry. I still should have known. I should have checked up on you when I realised he’d regenerated.” Stupid, Doctor. Stupid, stupid. She’d taught herself to think like her enemies, but then she didn’t utilise the skill.

Confusion crosses Jack’s face. He tilts his head to the side, licks his lips, swallows.

“You can ask me,” the Doctor prompts. “Whatever it is, you can ask me.” She’s not above prevaricating, but she wants Jack to believe he can ask.

“Who- Who do you think did this to me, Doctor?”

Ryan looks wide eyed from one to the other. She hasn’t discussed her suspicions with them, hasn’t discussed much of anything, too busy crashing around furiously searching, but they must suspect the same as she does.

“The Master,” she answers. She can’t decipher the emotions that cross Jack’s face, but guilt is among them. He hadn’t gone searching for the Master alone, had he? That would be unconscionably stupid for any human, but particularly for one the Master could sense coming streets away.

“No.” Jack’s soft word breaks off her thoughts. “It wasn’t the Master, Doctor. It was you. A different version of you.”