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This is the one problem I have with Clara. They all had a certain relationship with the Doctor that was touching and sweet in different ways, but Clara and the Doctor really didn't have that definite chemistry because he sees her as more of a mystery than a person.
"Just let this old box gather dust. No one can open it, no one will even notice it. Let it become a strange little thing standing on a street corner. And over the years, the world will move on, and the box will be buried. And if you wanna remember me, then you can do one thing. That's all, one thing. Have a good life. Do that for me, Rose. Have a fantastic life. "