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Molly could never really say that she knew Sherlock Holmes. Not a lot of people could.
But she knows him well enough to see that he was sad when no one could see him. Except for her, but to Sherlock, Molly was nothing.
She knows what that means, and though he'd never want her help, she offered it anyways, because whatever Sherlock's going through can't be easy.
He could at least say thank you. For the first time, she speaks her mind.
She doesn't believe it when he says that actually, he would like-
She knows him better than that.