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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.
I have a Tardis on a cloud. I like to go there in my sleep. Aren't any apples for me to eat. Not in my Tardis on a cloud. There is a lady all in blue. Holds me and says I'm the Tardis blue. She's nice to see and real to touch and she says My Doctor, I love you very much...