I don't usually put notes at the beginning of fics, but this does contain some spoilers for 'The Name of the Doctor' as well as some dialogue directly from the episode.
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She makes them some tea.
What else can she do? After she told the Doctor about her dream-séance thing, he'd gone from his 'what's going on' face, to his 'pondering' face and that face could last any length of time. Clara had seen it come and go in an instant, but she'd also seen it last for at least a few hours. She wasn't sure of the exact time; she'd taken a bath, eaten a sandwich and read a book while she'd been waiting. He'd kept the same far-off look every time she'd checked on him until he twirled into the kitchen while she'd been making tea and asked her if she'd ever considered seeing a unicorn. (They'd ended up stopping an assassination but that wasn't the point.)
She asked him about the woman with the space-hair. Clara had found that asking questions while his pondering-face was on served two purposes. Questions seemed to help him think, as his explanations tended to jog some idea or another. It was also the best time to learn things about him. When the Doctor was distracted, he let things slip. Little things like having a granddaughter or saving some planet twice before. It was one of the only chances she got to learn things without having to go though layers of distractions and deflections. His answers were vague and distracted.
"River asked Vastra for the exact words, what were they?"
She took the two cups and carefully moved to the living room. "The Doctor has a secret he will take to the grave," she recited. "It is discov—" the word died a quick death.
The Doctor was crying.
He…he was…crying.
Clara had seen him yell. She had seen him leaping for joy and bowed with pain. She had seen him ready to die; she had seen him run in fear. But this?
This?
"Doctor…" What…what can she do? She isn't his nanny; he doesn't have a skinned knee or boy trouble. What…what can she do?
"And if was Trenzalore, it was definitely Trenzalore?" She has heard this sound before, this fading of words before they can dissolve into sobs. She heard it at two funerals, she heard it in her voice, in the voices of people she loves, before they broke and the tears flowed.
But this is the Doctor…
"Yeah," she says, because she was asked a question and what else can she do? Her self-proclaimed Protector runs his hands over his face as though to physically hold his composure together.
"Oh, Damn…" She can see him break, just a fraction before he shakes himself and stands. Then the Doctor…apologizes.
And runs.
The door slams shut behind him and there she stands, with two full cups of fresh hot tea. What can she do?
Well, this at least has an answer she knows. Clara sets the tea down and goes after him. Out the door (which she locks behind her, who knows when she'll be back) and up to the bright blue phone box on the corner.
She doesn't go in. Not yet. She has never seen the Doctor even close to tears, let alone actually shedding them. She doubts many have. When someone breaks composure, sometimes you go after them to comfort. Artie was like that. He fled so he could accept the comfort in private, without being embarrassed. Angie was the opposite, fleeing because she truly wanted to be alone until she sorted things herself. Clara had no idea which would better help the Doctor, but she wasn't about to rush in either way. A few minutes to gather himself. Just a few minutes, and then she'd go in.
The TARDIS door opened on its own.
Clara glanced up at the ship. She could take a hint. Carefully, quietly, she slipped inside. The Time Lord wasn't bent over the console as usual, though she wasn't entirely surprised. She went down the nearest staircase, gently though. Listening for any sounds of distress.
If she heard crying, she would stop. No one wanted to be seen crying. Comforted, possibly, but not seen. Not like that.
He wasn't crying. He wasn't on the verge of crying, something Clara was thankful for. He was just…sitting. Not crying, yes. But not composed. Not really.
She gave him a small smile. "Well?" Explain or flee. Distract or deflect. How is this going to go? Just let me know what I can do.
He looked at her, then back to the console above.
"Trenzalore."