This is what happens when Scientologists come after you…

When John Sweeney made a TV documentary on the controversial church, he ended up followed, threatened by its leader, and on the wrong side of John Travolta. He tells his story – and asks what Katie Holmes can expect

Sinister strangers in big SUVs following you around 24/7. Men in dark glasses recording your every move. Your own most private space invaded, your mind probed, your sanity questioned, your loved ones spied on. Katie Holmes, welcome to my world. I would not want my children to be brought up in the Church of Scientology. I have actually had nightmares about that, so I think I can understand a little of what Katie is going through; why she fears what might happen to Suri if she had stayed in the Church that likes to wear dark glasses.

Poor Suri – a 6-year-old girl whose mum and dad are now at war. I feel desperately sorry for her, and her mother. Her father believes he is defending his religion, which he thinks is a force for good. That has not been, to put it mildly, my experience of the church that L. Ron Hubbard created.

When I went to the wars for a living, I was gassed, shot at, shelled, bombed and had two sticks of dynamite shoved up my nose. But never did I feel such fear for my grip on reality as I did investigating the Church of Scientology for the BBC's Panorama.

Five years ago I spent weeks at the centre of the church's attention. Private investigators whom I believe were working for the church chased me around the streets of LA, invaded my hotel at midnight and put me under surveillance at breakfast. Strangers spied on my wedding and knocked on the doors of my neighbours.

In the end, I lost it, doing an impression of an exploding tomato. I was wrong to lose my temper and I have apologised. John Travolta reportedly phoned up the BBC director general to complain about me. So I can only wonder at what Katie Holmes is going through now she has decided to divorce the church's number one apostle, Tom Cruise.

In the 21st century, everyone has a right to believe in anything or nothing. But not everything that claims to be a religion is a religion. It could be, for example, a brain washing cult. For a start, a religion must be honest about what it believes in. Scientologists believe in a space alien Satan called Xenu, but if you ask them, their spokesmen deny it. The church, to be fair, says on one of its websites that I am "genuinely evil". Thank you very much.

The very worst thing for Katie – according to former members of Sea Org, the church's holy order, that I've been in touch with in the past few days – will be the terror that her own secret thoughts about sex and love and despair may come out into the open. Scientology's version of confession is "auditing" using the E-meter, a kind of 1950s lie detector. What the Church often does is record E-meter sessions "for technical purposes".

If you turn against the Church, your secrets can come out. A former Sea Org member, Amy Scobee, after she left in 2005, was denounced as "The Adulteress" by the church's magazine Freedom, which accused her of "wanton sexual behaviour".

She told me: "It was difficult as a woman to deal with the backlash from the church. They hired private investigators stalking me, magazines were published to slander me." Her most intimate confidences were leaked. "The details of how I had sex with my husband before I got married is not something that should go to a newsp aper reporter. They made it the world's business, by issuing it on the internet and in a magazine that went to 100,000 or more people." The church denies breaching Amy's privacy or the sanctity of the confessional.

After Cruise married Holmes, they went on honeymoon with the leader of the church, David Miscavige. Cruise and Miscavige are great friends. They are both short men, like motorbikes and are deeply into Scientology. Ex-Scientologists claim that Miscavige is obsessed with sex and especially other people's sex lives. He is the potty-mouthed pope of a very peculiar religion, they say, sending cryptic text messages to his underlings such as "YSCOHB" – translation: "You Suck C**k on Hollywood Boulevard". This is the word of the Church of Scientology. The church denies that Miscavige abuses staff with obscene language, saying the allegation is beneath contempt.

Amy Scobee's book Scientology: Abuse At the Top says that at the church's headquarters in the California desert: "The confessional booths are set up with video cameras positioned to be able to see the E-meter and the person confessing simultaneously on a split-screen monitor."

She claims she confessed to a sexual act which Miscavige then knew about. "I couldn't believe that Miscavige made this incident a joke around the base. This was not only embarrassing but a serious invasion of privacy and a violation of the priest-penitent relationship the church is meant to honour." The church denies any breach of the priest-penitent relationship.

The church is accused of spying on Katie, of stalking her, of putting a big white SUV outside her safe house in Manhattan. It denies it, saying it has nothing to do with the church.

They spied on me. I know that for a fact because the man who led the spying team – Mike Rinder, the head of the church's secret police, the Office of Special Affairs – defected to us in 2010 and told me so on Panorama.

They spied on me in Britain. I've heard from a solid source that the church hired a team of private eyes here. I know the name of the company and have asked the House of Commons select committee on private investigators to look into it, with no success. The church denies spying on me.

They spied on me in the US. Rinder and Tommy Davis – the chap I exploded at – tracked us down to our hotel in Florida, and then Mike tailed us across the US to San Francisco and then to LA. He knew where we were, what we were doing, who we were talking to. And at every stage he reported back to David Miscavige.

The text messages between the three men are beyond surreal. Davis boasting: "We've worked out exactly what we are going to do to handle Sweeney terminatedly. Ml, Tommy". "Ml" stands for "much love".

After Anne Archer, a leading Scientologist and the actress whose bunny got boiled in Fatal Attraction, and I clashed when she asked me: "Do I look brainwashed to you?" and I lifted my eyes to the heavens, this message was sent by Miscavige's office: "Were these ass rippings on camera? What did he think when Anne went after him for saying her son is brainwashed. Any other details you Generality infested CSMF?" This was later translated for me as: "C**k Sucking Mother F****r".

Frustrated that the church's agents could not stop me from doing my job, Miscavige's office sent another message saying: "YS! (You Suck) You just can't work or do can you? YS (You Suck) YS (You Suck) YS (You Suck) YS (You Suck) YS (You Suck)!!!!!!!!!!!!!!!!!!!!!"

David Miscavige says the suggestion that he or anyone in his office monitored any such operation, communicating with Rinder and Davis, is absolute nonsense.

Rinder told me this week: "David Miscavige seeks to control everything around him, including the life of Tom Cruise and by extension Katie and Suri. He helped arrange hiring Scientologists to work for Tom and of course deployed Sea Org members to do all sorts of things for Tom, from building theatres and sound systems and interior decorating in his house to designing custom SUVs, buses and motorcycles.

"The story about this being a 'marriage' of three people, with Miscavige as Tom's 'man-wife', is close to the mark. Anyone would find it intolerable to be in a marriage like that and it's surprising it has lasted this long."

Rinder concluded: "Hopefully Tom will wake up and realise the insanity he has been part of. It's probably too late to save his marriage, but he may be able to resurrect some of his own dignity by stepping out of the shadow and freeing himself from the manipulation of Miscavige."

Do not doubt the power of the Church of Scientology. I want to write book about my experience of the Church, and thus far every single publisher we have approached has turned me down. It is worth billions of dollars and has friends in high and low places, as well as those who seem prepared to give it the benefit of the doubt or to work for it: Hollywood A-listers, the law firm Carter-Ruck, senior British police officers, a former Murdoch newspaper editor, TV stars like Jonathan Ross who wrote in his biography: "I don't think Scientologists get a fair deal. Scientology doesn't seem much sillier or more harmful than any of the bona fide longer-running religious games in town."

Then there is the energy minister, Charles Hendry. The Conservative MP, whose Sussex seat borders Scientology's UK base in East Grinstead, told the Commons in July 2005: "Although Scientology may be very controversial, undoubtedly, as human beings they do a great deal of good… It isn't a cult."

Mr Hendry said yesterday: "I am absolutely not a friend of Scientology. I have no connections with them except for the fact that 500 to 1,000 of them live in my constituency or just outside the border. I was speaking on their behalf as a constituency MP. My words were very selectively quoted by John Sweeney in the Panorama programme."

By her actions, Katie Holmes appears to disagree. She must be very afraid, but I can't help feeling that what she is doing is right and brave and good.

John Sweeney is a reporter for the BBC's Panorama