In 1955 MacNaughton moved back to London, and was cast as Able Seaman McIntosh in Seagulls over Sorrento and as Haggis in the 1956 science fiction film X the Unknown.
[1] He then appeared in three episodes of the British television comedy show Hancock's Half Hour and had small roles in the films The Silent Enemy and The Safecracker.
[3] MacNaughton continued to act in numerous small roles for television and film, including Dr. Finlay's Casebook and Redcap in 1964 and The Avengers in 1965.
In 1966 and 1967 he directed all 52 episodes of a BBC series called This Man Craig, which was set in a large comprehensive school in the fictional Scottish village of Strathaird.
In 1969 MacNaughton directed and produced the first series of Spike Milligan's Q, a surreal British comedy television sketch show consisting of seven episodes.
[1] Having accepted the job of director and producer, MacNaughton announced to the Pythons' dismay that he had to take a holiday and would be unavailable for the first four shows, which were consequently directed by John Howard Davies.
[1] Initially, there was some friction between MacNaughton and the Pythons because of their close involvement with the way the show was directed, but by the end of the first series he had become one of the team and his contribution was significant.
In the same year, MacNaughton directed the group in the first of two German specials filmed in Bavaria called, Monty Python's Fliegender Zirkus.
In 1976, MacNaughton directed another pilot comedy sketch show called Out of the Trees, starring Monty Python alumnus Graham Chapman.
[3] In 1996 he directed Australian composer George Dreyfus' comedy, The Marx Sisters in Bielefeld and in 1997 Gerhard Baumann's Nyx in Munich.
In 2001 MacNaughton suffered extensive injuries in a car accident while returning to his home in Munich, Germany from the first night of a translation of Alan Ayckbourn's play Seasons Greetings in Hall, Austria.