Pemberton wrote the 1968 Patrick Troughton story Fury from the Deep (which he subsequently novelised for Target Books). The story, now missing from the BBC archives, was based on an earlier stand-alone radio serial he had written called The Slide, starring future Master actor Roger Delgado. It introduced the Doctor's trademark sonic screwdriver. He was also story editor of season five opener The Tomb of the Cybermen.

In 1976 Pemberton wrote the audio drama Doctor Who and the Pescatons for an experiment in Doctor Who on vinyl record and an early spin-off from the programme. The production was aimed at children and is heavily based on ideas Pemberton had used for Fury from the Deep. He later novelised The Pescatons, which was the final Doctor Who book published under the Target imprint. He had previously appeared as an actor in the series, in a non-speaking role as a scientist in the 1967 story The Moonbase.