SUMMARY: Can you light a spark?
It's been there, ever since he grabbed her hand and told her to run. She just didn't want to admit it, not when she had Mickey. It would have been wrong. He wasn't exactly her type either, and then there was the age difference to consider. Especially after he told her how old he actually was. When she began to realise – and acknowledge – the extent to her feelings, she tried to relegate them to being a bad case of 'alien hero worship.' After all, who else could take her through time and space without reminding her of her distinct lack of educational qualifications? He might call her a 'stupid ape,' but that's more indicative of his own perceived status in the universe.
She's not entirely sure whether her feelings are reciprocated. There are times when he is aloof, not just to her but also to people they meet on their travels. He can leave her alone in the TARDIS, forcing her to make her own entertainment, sometimes for days. Or his mood will be so lousy she won't want to be anywhere near him, never mind how she feels.
But then, sometimes, she'll catch his eye and he'll catch hers. And it will feel like he's slowed down time. His eyes will darken as he leans towards her. Her breath will catch as she thinks, "This is it! Finally!" And then he'll grin that huge grin of his, as though he's let her into some huge secret, whirl away from her, and it's on to the next adventure.
It's only with time – what irony – that she learns the truth. He prefers solitude to the uncertainty of love. But by then, she's a universe away, and he's not the man he was when they first met. Moreover, despite his mastery of time, that part of their lives is gone forever.