2

In A Good Man Goes To War, they wonder about Amy's baby:

DOCTOR: It doesn't make sense. You can't just cook yourself a Time Lord.

VASTRA: Of course not. But you gave them one hell of a start, and they've been working very hard ever since.

DORIUM: And yet they gave in so easily. Does this not that bother anyone else?

DOCTOR: Amy. She worried the baby would have a time head. She said that

VASTRA: Only you would ignore the instincts of a mother.

DORIUM: Or the instincts of a coward. This is too easy. There's something wrong.

DOCTOR: Why even do it? Even if you could get your hands on a brand new Time Lord, what for?

VASTRA: A weapon?

DOCTOR: Why would a Time Lord be a weapon?

VASTRA: Well, they've seen you.

Then he sits having a spooked look on his face and says

DOCTOR: Me?

which made me think why did the Doctor look scared after Vastra said "they've seen you"? Was it the dangerous things things he did in his past incarnations?

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    Tip: proper names (Amy, Vastra, and - in the context of this show - Doctor) should begin with capital letters. Good job on the quote formatting though. – Rand al'Thor♦ Apr 15 '16 at 14:12
12

More precisely, they've seen what a Time Lord can do. Every time they or others tried to strike him down he wound up laying them low.

... And what disturbs him (scared isn't quite the word) is that, despite his name being the Doctor, his victories and reputation are resulting in him being known as a warrior and destroyer, rather than a healer.

From the same episode:

THE DOCTOR: You think I wanted this? I didn't do this! This- this wasn't me!

RIVER SONG: This was exactly you. All this. All of it! You make them so afraid. When you began all those years ago, sailing off to see the universe, did you ever think you'd become this? The man who can turn an army around at the mention of his name. "Doctor": the word for "healer" and "wise man", throughout the universe. We get that word from you, y'know. But if you carry on the way you are, what might that word come to mean? To the people of the Gamma Forests, the word "doctor" means "mighty warrior". How far you've come. And now they've taken a child, the child of your best friends, and they're going to turn her into a weapon, just to bring you down. And all this, my love, in fear of you.

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    becoming what? the victories are heroic – Andrew Casali Apr 15 '16 at 14:38
  • @andrewcasali Becoming known as a warrior and destroyer rather than a healer. – Shadur Apr 15 '16 at 14:39
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    @AndrewCasali: What in heck is "heroic" about double genocide? – Lightness Races with Monica Apr 15 '16 at 19:22
  • "We get that word from you, y'know" FYI, that idea that the word "Doctor" comes from the Time Lord's name is something Moffat's had in his back pocket for years - he first mentioned it on one of the Doctor Who newsgroups WELL before the show came back. – VBartilucci Dec 6 '18 at 13:39
1

I agree with the first answer, but I just like to add:

We know that everyone who travels with The Doctor is under his "duty of care", which he takes very seriously. Every time something happens to one of his friends and he knows it's his fault, he gets very upset. And that's also often his excuse to go rescue someone with fury even when the situation looks impossible.

When Vastra points out, that they've seen him and that's the reason why his best friends daughter was taken, I believe that it scared him to realise, that he had caused that much suffering to the people he loved.

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