Queried about "The Master"'s elliptical narrative, in which Phoenix's feral drifter Freddie Quell comes under the spell of Hoffman's intellectual prophet Lancaster Dodd, Anderson said, "I think we were just trying to tell a love story between these two guys. We had a lot of scenes that weren't about that and we took them out."
The inevitable Scientology-laced questions emerged, with Anderson revealing that he had already shown the film to Tom Cruise and that "we're still friends – the rest is between us." On how much the film's narrative draws on Scientology and the life of L. Ron Hubbard, the filmmaker said, "That's not an elephant in the room. This is a character that I created based on L. Ron Hubbard, there's a lot of similarities to the early days of Dianetics... I don't know a hell of a lot about Scientology today but I know about the beginnings of that movement and it inspired me to use it as a backdrop for these characters. I can't be any more unambiguous than that."