In the 1980s Miller spent two years researching Bare-faced Messiah: The True Story of L. Ron Hubbard, a posthumous biography of the science-fiction author who had founded Scientology. The book challenges the official account of Hubbard's life and work promoted by the Church of Scientology and it was serialised in the Sunday Times.

While researching the book in the USA, Miller was spied on. His friends and business associates also received visits from scientologists and private detectives. Attempts were made to frame him for the murder of a London private detective, the murder of American singer Dean Reed in East Berlin and a fire in an aircraft factory. Senior executives at publishers Michael Joseph, and at the Sunday Times, which serialised the book, received threatening phone calls and also a visit from private investigator Eugene Ingram, who worked for the Church. Another private investigator, Jarl Grieve Einar Cynewulf, told Sunday Times journalists that he had been offered "large sums of money" to find a link between Miller and the CIA.

In his capacity as Hubbard's biographer, Miller appeared in three British television documentaries:

• Facing South: The Cult Business broadcast on TVS (southern England regional TV), November 1987
• The Big Story: Inside the Cult made by Carlton TV and broadcast on ITV, July 13, 1995
• Secret Lives: L. Ron Hubbard made by 3BM and broadcast on Channel 4, November 19, 1997