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She’s not comfortable. This is a Timelord, sure, but it’s not her timelord. She’s used to being able to infuence him, to go where she knows they should instead of where he thinks he wants. This one is busy drowning out the sounds already inside his head leaving no room for her to reach him. And he’s deeply unhappy, at cross-purposes with himself, to a degree she’s not felt since... well, since the Doctor, at the end of the Timewar. Even though he doesn’t let her in, she cannot help letting his feelings seep into her.
He doesn’t know what she really is, of course - none of them do. They think they are in control, and most of her sisters have seen no reason to let them know otherwise. They call themselves Timelords, and yet they have never understood that they travel inside of Time itself, and that their lordship is subservient to the rule of her and her sisters.
The humans have a saying that noone who enters Faery returns unchanged. Of course, “Faery” is just a word they have for places that don’t exist within their knowledge of the universe, and she doesn’t mind being called so. She finds it amusing that these short-lived ones, brief flickers of flame so quickly and easily extinguished, have understood her better than he who has travelled in her for centuries. She knows she can change this one too; she has all the time in the world - to be specific, she has all the time in all the worlds. To him, the journey will appear to take no longer than expected; to her, the passing of time is fluid. She plants the seeds of the thoughts that will keep her Doctor alive for her to return to. She’s already made sure that Jack (and oh, how difficult it is for her to look at him now!) will bring him to her. And all will be well, as it will ever have been. More or less.
She’s sorry for them both. She’s had him for long enough that her feelings echo in his hearts, and as looking as Jack pains her, so it does him. She wishes it were otherwise - it would be good to see them smile at one another again. He would be happier if he could have a companion who could travel with him through the ages, one that will not age and die before his eyes. And yet, looking at Jack is as looking at the sun shining and reflecting through a million broken mirrors. When she sees him, there is no room at all for her to see anything else. And she wants to see her Doctor.
She bides her time, waiting for the unhappening.