The Church of Scientology is a deeply strange organisation and, appropriately enough, Louis Theroux has made a strange film about it. It works as a companion piece to another documentary, the one that I think is the definitive takedown: Alex Gibney’s Going Clear: Scientology and the Prison of Belief, from 2015. It’s an interesting, if flawed piece of work; Theroux’s opaque manner masks an uncertainty as to exactly what he wants to say, and he finally seems to turn on his own chief witness.

Theroux’s Scientology movie is undoubtedly a smart piece of what could be called improv-ocation. He shows up in LA, advertising his intention to film a series of scripted and unscripted scenes recreating key moments from the life of the Scientologists’ sinister chief, David Miscavige. (Theroux may here have been inspired by Josh Oppenheimer’s modern-classic documentary about the Indonesian tyranny, The Act of Killing.) He will audition actors, film the audition process, and use as his adviser a famous apostate and whistleblower, former Scientologist enforcer Marty Rathbun – a man now hated in the church for his betrayal.

Inevitably, the church gets wind of what he’s up to and begins the usual legal sabre rattling and sending round people with movie cameras for counter-doc harassment, a familiar Scientology tactic. And it seems very possible that at least one of the actors auditioning for Theroux’s movie is a Scientologist mole!

There are some intriguing things about this, not least the extraordinary and very convincing improvised performance that Theroux and Rathbun get from the actor pretending to be Miscavige, bullying and brutalising the terrified faithful. Now, his scenes don’t prove anything as such, but Rathbun says they’re very convincing. Yet here’s the problem. Theroux has an ambiguous attitude to Marty Rathbun.

There is a weird moment in which Rathbun is reluctant to let actors in an improvised scene applaud the picture of Scientology founder L Ron Hubbard. He says it’s because he wants to lead them away from the submissive mindset – though could it be because he’s still brainwashed, still can’t bear to let the Dear Leader be mocked, even by implication?

Opaque approach … My Scientology Movie. Photograph: Flat Creek Films/BBC Worldwide

If he is still traumatised, this does not earn Rathbun sympathy from Theroux, who asks him again and again about his behaviour while in the church. Theroux almost seems to be having it both ways: using Rathbun’s invaluable inside knowledge, while sneakily setting him up to be confronted for the bad stuff he did while a top-ranking Scientologist – even though Rathbun has admitted to it and is now publicly working against the Scientologists. He is, after all, helping Theroux with this film. And what thanks does he get?

At one stage, just after Rathbun has been horribly monstered by some unspeakable Scientology footsoldiers, Theroux chooses this moment to deadpan a question at him, saying that this was only the sort of aggressive behaviour Rathbun himself used to get up to. Rathbun gets furious with Theroux’s apparent bad faith. It’s an unsatisfying aspect to the film.

Well, there are some gloriously surreal moments. Just when Theroux starts interviewing Rathbun in a hotel room opposite the pool, a woman in a bikini suddenly appears outside the window, demands they stop filming, but then coyly announces she is an actress. She is, in fact, Paz de la Huerta, who starred in Gaspar Noé’s film Enter the Void and the TV drama Boardwalk Empire. She then just disappears from the film. It is Alice in Wonderland stuff.

Theroux also sheds more valuable light on how very important LA and the movie industry are to the Scientologists. It is a cult that depends on the desperation of those who have come to Tinseltown to chase their dreams; it is a fantasy belief system that is pure B-movie sci-fi nonsense. Yet Scientology thrives by siphoning off some of the escapist-aspirational energy generated by the Hollywood dream factory. And poor Tom Cruise is still at the centre of it all.

Have the Scientologists amassed a personal hold over their famous and non-famous believers during the confessional “auditing” process? It’s hard to say. Theroux shows us once again that strange footage of Cruise shaking hands with Miscavige and sort of embracing him at the same time. Cruise is like a pupil at a minor public school who is expected to shake hands with the headmaster who has just caned him. Theroux doesn’t add anything substantial to the Gibney documentary, but he reiterates the sheer nastiness of this horrible corporate cult.