The Doctor's admission that he doesn't know what to do next stirs up unexpected fear in Will. His Doctor, the one he knew first, never would have said anything like that. Even if it were true at some point, Will's certain he never would have admitted it even then. And so he just watches the Doctor for a moment, expression stricken. He has no idea what to say to that.

But after the Doctor breaks the silence, he eventually manages: "All right." But he doesn't move. Subconsciously, he's still waiting to follow the Doctor's lead.