How well does Clara Oswald know the Doctor? Intimately. Almost as well as she knows herself. But perhaps not as well as she thinks she does.
Clara’s understanding of the Doctor primarily comes from two things. Firstly, and generally speaking, Clara has an enormous propensity for empathy. She is very good at reading people, and this skill is not just limited to the Doctor. ‘Why are you so sad?’ she asked Robin Hood, cutting his raucous laughter and flirtation short. But as of series 9, we know that she spends a lot, if not most, of her time with the Doctor. Sure, she gets dropped off on Earth to teach, and she still has her own apartment, but their relationship this series no longer feels like a ‘Wednesdays-only’ arrangement. They are very much in sync, and attuned to each others’ feelings, as only those who live, travel and play together can be. And this doesn’t go unreciprocated; the Doctor’s words to Bonnie in The Zygon Inversion tell us that he can read Clara’s face just as well as she can read his.
Secondly, Clara has a deep understanding of the Doctor by virtue of how very similar they are in character. We have been shown this similarity onscreen, and told it off-screen by Moffat himself. “Because he always assumes he’s going to win”, said Clara to Missy in The Witch’s Familiar, when asked how the Doctor always managed to survive despite the odds against him. In Heaven Sent, the Clara hallucinated by the Doctor in his ‘storm room’ confirms this in a fashion, as she repeatedly asks him “How are you going to WIN?”
Where Clara’s ability to pre-empt the Doctor’s next move falls short are in areas directly relating to her. She is the wild card in her own equation in figuring the Doctor out. When she says to the Doctor in Face the Raven, “Your reign of terror will end with the sight of the first crying child and you know it”, she genuinely believes that of him. When he replies, “No, I don’t”, she construes it as a heat-of-the-moment declaration, but that when push comes to shove he will inevitably cave to the weight of his conscience.
However, Clara underestimates just how much of the Doctor’s self-restraint is a direct effect of being around her. The Doctor is nothing without an audience, and Clara, at this stage in his life, is his best and most importance audience of them all. He enjoys showing off for her, making her laugh, and constantly seeks her approval . Her approval meant so much to him that it changed the course of the Time War; he didn’t press that button for fear of disappointing her. Clara’s comment to him in the Viking village, “You just decided to stay” makes it sound as if the Doctor arrived at that conclusion by himself, and maybe she truly believes that he did, but in actuality it was her pushing him every step of the way to do the right thing. Yet again.
How is it that, for someone who purports to know the Doctor so well, Clara is so blind when it comes to realising how far he will go to save her? And she is blind to it; when the Doctor broadcasts his intentions to destroy Skaro if Clara Oswald is not returned to him immediately, she is as surprised as Missy that her safety could move the Doctor to such desperation. Similarly, the possibility never even crossed her mind that she could have been the reason the Doctor held out (and on) for 4.5 billion years in the confession dial.
So why this particular oversight of Clara’s?
Perhaps Clara figured that there are certain lines even the Doctor wouldn’t cross. These lines are ones she has drawn for herself, and by virtue of her perceived knowledge of the Doctor and how alike they are, she believes that these lines exist just as clearly in his mind. But what she didn’t count on was that repeat loss, over his inordinately protracted life, has long since blurred those lines for the Doctor. And because he’s lost so much, he holds onto what he has that much tighter.
Clara could not have anticipated this, because this is so far beyond the scope of her own experiences. Over 2000 years of watching everyone else die, leaving him, and always him, behind. And Clara isn’t just anyone. She is his Second Chance, and goodness knows he never gets those, so he’s not going to let this one go. Not even if it means going against everything the title of ‘The Doctor’ stands for.
So to say that Clara brought out the worst in the Doctor is both patently true, and a gross oversimplication of their relationship. She brought out the worst in him in a way that neither one of them could help. He couldn’t help that her existence was so paramount to his own, and she couldn’t help her all-too-human lifespan. As long as she is around, the Doctor could count on her to talk him off the proverbial ledge, but all bets are off as soon as she is out of the picture. He needed to learn to live without her, and short of a memory wipe, there was nothing that could have convinced him to let Clara Oswald go.