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The Great Intelligence, once on Trenzalore, entered the Doctor's timestream (see "The Name of the Doctor") & could therefore appear anywhere in time & space that the Doctor had been. Indeed, as explained in that episode, the Great Intelligence entered the Doctor's timestream for the specific purpose of "vandalising" it at a very large number of spacetime locations. Clara Oswald, who followed the GI into the timestream, in order to repair the damage, also appeared at a very large number of spacetime locations, though the Doctor was only rarely aware of her.