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On screen, this has never been confirmed beyond some innuendo by River Song in "The Impossible Astronaut" et al. The ending of "The Dying Days" (novel) suggests that the Eighth Doctor sleeps with Benny Summerfield, but this too is open to interpretation. Amy's attempted seduction of the Eleventh Doctor in "Flesh and Stone" is the only time a companion has been shown on screen attempting to initiate such a thing, though Martha in "The Shakespeare Code" makes overtures when she and the Doctor share a bed.