He comes back when she calls him. Before she can send him away again, he says, "Explain it to me. Please. Explain what I did wrong."
He's trying to be a good man; his face is so vulnerable and so full of need that she can't turn him away.
The second time, he holds her hand through it.
"I'm sorry," the Doctor whispers, his mouth millimeters from her ear, his chest pressed against her back, and the scent of her hair will forever bring him back to this moment, the moment where he presses her palm against the lever and they set the infested planet below them on fire. "It's the choice we must make."
It's exactly the sort of comfort and support she'd asked from him; when she hugs him, he only flinches for a moment before his arms twitch upwards as though he were preparing to hold her. It was the right choice, a difficult choice but a necessary one, and it's made easier by his being there with her.
It takes Clara weeks to be horrified over not having been horrified.
Danny touches her with a sweetness she doesn't think she deserves. By the time she had thought to be horrified, she'd had a rifle hefted to her shoulder and half the crew of a broken down interstellar freighter behind her, begging her to kill the shadowy blood-wet thing that had once been their captain.
Hero, they whispered. Brave. Confident. Right.
She wakes up smelling ozone and charred flesh; Danny pulls her closer in his sleep and murmurs something against her neck.
The Doctor would never admit it, but there are two reasons he needs a companion. First: to share the wonders of the universe. Second: to share the burdens.
He's good at sharing his burdens with her. He thinks he's getting better at sharing her burdens as well, and whenever she shoots him that look--disappointed, bright-eyed and sad--he is quick to take on whatever it is she wants him to take on.
He is getting better. He is learning. When she leaves him alone in his TARDIS, he knows he must if he wants her to keep coming back.
The third time, Clara doesn't have anyone to hold her hand. Pressing the button on the sonic to wipe the memories of the mind-controlled squadron attacking them--this time it's not a difficult choice, with the Doctor collapsed unconscious behind her. The soldiers turn into untrained civilians, though Clara has no idea how much has been wiped and frankly doesn't care, because in their confusion she finds the time and place to drag the Doctor back to the TARDIS and jam her hands into the telepathic circuits. It's just enough to get them into space, away from the quickly-deteriorating situation on the base they'd been trapped on for so long.
When the Doctor wakes up, she's kneeling beside him dabbing at a wound on his temple. He looks up at her in confusion and asks, "What happened? I don't remember-"
She smiles down at him with a confidence she's not sure she really feels. "It's fine. Everything's fine."
He looks at her with relief and trust, a broad smile on his face and pride in his eyes. She thinks maybe she should feel more confident.
Clara's concerns always center around others, and whether she can do something to help. And so Clara the au pair jumped into an alien's time stream to make sure he lived to save the universe over and over again, and Clara the English teacher helped him stop himself from committing a genocide against his own people. She's always been willing to make the sacrifice.
When the Doctor asks for her help in the choice between the death of a few and the death of millions, Clara no longer feels horrified at not feeling horrified. It's the choice they must make.
Clara holds his hand through it, and the threat is exterminated. Her thumb strokes the back of his knuckles, she leans into him, and when he stiffens against her, she murmurs, "We did good, okay? We did good."
"You'd tell me, right?" Danny asks one night, out of the blue.
It's a clear night and they're looking up at the stars, on a blanket up a hill just far away enough. "Tell you what?"
"If he's pushing you too far again."
Some of the stars are only there because of her. She's grown so much with the Doctor. These choices he'd been making--she knows she can make them now, too, and she can make better ones, with him standing with her. With a smile she pulls closer to Danny and says, "He's not."
She still travels with him purely for fun most of the time. And she finds it's easier to think of things as adventures, even when they do get into trouble, even when she does have to make the really tough decisions, because she knows she's a good woman. The Doctor may still not know enough about himself to call himself a good man, but she has faith in herself as a moral compass, and in the way she views the universe around her. He needs a teacher.
So when a species new to him threatens her home, a displaced species with weapons and so much anger, she finds it very simple to ask him to eradicate them. And when he frets that they're unknown and that maybe he could help them find a new planet instead, she takes his face in her hands and looks him in the eyes and says, "Do you trust me, Doctor?"
He nods. He nods and her hand strokes down his back as he does exactly as he's told. An unsettled part of him grows louder.
Later, he wakes up on the TARDIS floor. Clara is knelt over him with his sonic in hand and a frown on her face. He shakes his head to clear the fog, and when she reaches to stroke his cheek, he flinches at her touch. "Did you-"
The frown deepens. He wakes up on the TARDIS floor. Clara is knelt over him with his sonic in hand and pity in her eyes. He shakes his head to clear the fog, and when she reaches to stroke his cheek, he flinches at her touch. "Clara, please-"
She sighs. He wakes up on the TARDIS floor. Clara is knelt over him with his sonic in hand, smiling down hopefully. He shakes his head to clear the fog, and when she reaches to stroke his cheek, something inside of him forces him to stay still. He draws his mouth into a weak smile. "I don't remember," he says.
"Everything's all right," she says. "Trust me, okay? We did what we had to. Everything's all right."
We did what we had to, he tells himself. We. We. His smile turns into something real.
"Always so in control," Danny says, his face lighting up with warmth. Clara grins back up at him, her nose wrinkling, as she wraps her arms around him and leans up to kiss his jaw. "You ever gonna let me know what happens when you give it up?"
"Mm," she says. "Never going to happen."
It's been a long day; they're at the door to her flat, with the sun setting behind them. He laughs and holds her by the waist. "I think I can make you change your tune, Miss Oswald."
She slaps him on the chest, light and playful, scoffs. "You don't stand a chance."
"Probably not," he admits. "Still want to try."
Clara's right; he didn't stand a chance.
There's a beast in the man, a creature who is ruthless and raw power, an intelligence that is wielded without wisdom. There is nothing more dangerous than this, except for the woman who holds the leash.
She leans up and whispers in his ear, "Take me somewhere that needs us, Doctor." Later: he stands proud over ruins he's created, and when Clara touches her fingers to his jaw, he forces himself to lean into her caress for the first time.
Danny begins to suspect.
He asks her again if the Doctor is pushing her too far. Except this time, there's an undercurrent to the question, an assumption where he thinks he already knows the answer.
Clara can honestly tell him he's worrying about nothing. She's never felt this sure in her life. She's exactly where she needs to be.
When she tells the Doctor of Danny's suspicions, he pleads, "Let me watch him. I can look into-"
"No. Not ever."
But two days later, she's walking with Danny, her hand in his, and she feels a ghosting, invisible brush of fingers against her other hand. When she gets to the TARDIS, the Doctor is looking at her defiantly. "Could you tell?" he asks.
She slaps him hard across the face. "I said no."
He leans closer to her, and it takes all her grit not to step back; she'd somehow forgotten he's not completely tame, that this part of him could be turned on her. "You let him watch me. It's only fair."
She can't help the way her lip curls into a disgusted sneer, and she's fairly sure she wouldn't stop it even if she could help it. "That's not how this works. Do you even understand fairness?" Uncertainty flickers in his eyes before he clamps down on it, but he's not quick enough. Clara shakes her head and brushes by him. "I have to explain it, don't I?"
"You don't." He's standing lonely now, that same uncertainty blatant on his face and trepidation blatant in his stance. "Since you let him come here, I should-"
"No, I've had to lie to him about you already, I'm not doing it a second time." She leans against the console, her arms crossed, and dares him with a glare to argue against her. "You do it again and we're done."
It's enough to make him contrite, or at least afraid. She'll take the fear, it's as good as anything else. "Fine," he says, "I won't." He's trying to say it hard-edged, but she knows him too well and she can hear the shake in his voice. "I'm sorry. I should have known."
Clara's in more familiar territory here, and so she takes a step towards him. Her hands smooth down his shirt, heedless of the way he cringes at her touch, and she says, "Not your fault. It's why you need me around, isn't it?"
The Doctor looks at her with something that could be reverence or could be fear.
There is a beast. It needs love. It needs controlling. Clara understands her duty better now than she ever has; she was born to save him from himself.
Danny's suspicions continue until her heart breaks. There's no way she can keep the man she loves wondering like this; she makes the decision to let him go.
The Doctor had shown her the setting for memory wipes on the sonic, and it's necessary to use it before she asks the Doctor to implant a memory of a fight. "Something mundane," she says softly, tears in her eyes. "So he thinks we just broke up normally."
After, the Doctor hesitantly thumbs moisture off her cheek, but she can see he's unsettled more by what she'd asked than by how she'd cried.
The Doctor had shown her the setting for memory wipes on the sonic. He'd long since forgotten when he'd shown it to her.
He wakes up on the TARDIS floor.
Clara wonders at all the good there is to do in the universe. That there are choices she needs to make in order to do them--finally she understands the Doctor's insecurity over his own morality. She doesn't share it though. Her results are always right, she's saved more than she's killed, and when he finds himself worried, she gives him comfort in the best way she knows how. Some decisions are too important not to make on her own.
And Clara is not heartless; she tells him he'd had to forget, he'd been scaring her, this had been the only way, with a hand on his cheek to soothe away the confusion. If he still flinches at her touch sometimes, she simply does it again until he's calm under her.
Only once does she think she might have gone too far. He stutters on his knees, resting his head in her lap, murmuring, "Miss--Miss," over and over again when he can't find her name anymore. "Sorry, I know you, I love you, I'm sorry you're my--you're--"
That he remembers the most important things is enough for her. "Shh," she whispers back. "You're my Doctor. I love you too."
"Am I a good man?" He stares down at her intently. Her hands stay on him and he doesn't get a vote about it but he's learned to keep still when she touches, in spite of the way it makes everything feel too much. The Doctor thinks he can remember another one, some other man who might have been good, who didn't have to focus so much on fitting rightly with her.
He thinks he might be the better man because it's not as easy for him.
"You try," she says. Her open palm is against his neck. He tries to think about anything but the fact that she's too warm on his skin. "And that's what matters."
He can still see the universe and time itself in ways nobody else can, and in time he figures out how to share that grace with her, too.
There is a beast, the universe knows, and she has the most beautifully terrifying pet.