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Twenty minutes into my visit to Saint Hill Manor last week, a Georgian house on the edge of East Grinstead and about an hour on the train from Victoria, a uniformed man with a dog approached me, and he wanted to check a few things.

“You are a Scientologist?” he asked, with a Polish intonation.

“No, I’m just having a look around.”

“So you are a guest,” he said. “We like to know who is here.”

The staff at Scientology’s UK headquarters are alert to the danger posed by outsiders, their movement the subject of criticism from former members (“defectors”), children’s campaigners and courts around the world since its birth in the 1950s. Scientology’s beliefs about a dictator alien called Xenu who blew up his people 75 million years ago by exploding volcanos with H-bombs have attracted ridicule since they were published against the church’s will, and advocates have long denied accusations that their movement is a cult or a front for a money-making operation.

The announcement this week that Katie Holmes and Tom Cruise had agreed divorce terms rounded off another period of intense scrutiny of the church. Speculation that Holmes was motivated by concerns about her daughter, Suri, being educated by Scientologists and initiated into a secretive group called Sea Org were given credence by the couple’s joint statement, in which they sought to “express our respect for each other’s commitment to each of our respective beliefs”. An insider told celebrity news site Radar: “Suri isn’t permitted to be exposed to anything Scientology-related and this includes going to any Scientology churches, parties, etc. Katie made sure this was ironclad.”

Since the divorce, journalists have been queuing up outside Saint Hill, where Scientology’s founder L Ron Hubbard lived between 1959 and 1966.

But the story of Scientology’s relationship with children is better told if you make a 10-minute car journey to Greenfields, a small independent school perched on the corner of the Ashdown Forest, where some of the future leaders of Scientology are being educated.

The sign outside describes it simply as an “Independent day and boarding school from 2 to 18 years old”, and the students mill about in ordinary green and brown school uniforms. But the locals in Forest Row have long known that Greenfields is the school of choice for the staff at Saint Hill. In a landmark High Court case in 1985, Justice Latey said that “the church exercises a strong influence [at Greenfields], if not indeed control.” Greenfields now describes itself as “completely non-denominational” welcoming “children of all faiths” although it is thought that many of the teachers are Scientologists.

Set back from the road along a private drive, the school is housed in a Victorian mansion. It uses the Study Technology learning method devised by Hubbard, which involves allowing students to learn at their own pace and using clay to work out how to visualise challenging questions, and is licensed to Applied Scholastics International, an organisation which promotes the use of Hubbard’s teaching methods all over the world. Hubbard is described as an “Educator and Humanitarian” in the school magazine. Justice Latey called him a “charlatan and worse”.

A report from the Independent Schools Inspectorate last year said the school achieved “good” academic and pastoral standards, but that just eight of its 101 students are in the sixth form. What it didn’t say is that, almost every year, a few students leave Greenfields and never come back to complete their studies.

The Standard has learned that the students who go are not transferring to local sixth form colleges but travelling to America to enrol at Sea Org — the secretive arm of Scientology which has been the subject of the most frightening allegations made about the church. Former students have told the Standard that Greenfields students sometimes leave the school before age 16. The children seem to vanish — cut off from their non-Scientologist friends when they are at Sea Org, where Facebook and all social networking are banned. Most shockingly of all, the Standard has been told that within two years of their teenage classmates going to Sea Org, news reaches Greenfields that some of their former peers have married fellow Scientologists.

Sea Org is described as “the church’s equivalent of a religious order” and has about 6,000 members, who maintain the naval-style customs, uniforms and discipline developed when the elite group was based on a fleet of yachts at sea. Nowadays just one boat — Freewinds — remains and Sea Org members operate mainly on land, at a complex in Clearwater, Florida and Scientology’s highly guarded Gold Base in the California.

A number of women over the years have alleged that they were put under pressure to abort their babies by officials at Sea Org as a result of the no-children policy — claims the church has always denied. Gary Morehead, a former head of security at the Gold Base, has said he developed a “blow drill” to track down Sea Org members who tried to escape, which sometimes involved using physical force. He says that in 13 years, his team caught upwards of a hundred members but the church says that blow drills do not exist.

It is well known that members of Sea Org are required to sign contracts for up to a billion years of service, and that those trying to leave can be presented with a “freeloader tab”, charging them retrospectively for thousands of pounds of counselling they have received as a member.

Fred, 20, who left Greenfields four years ago, told the Standard that about 10 pupils left for Sea Org in the two years he was there.

“Most of them left once they had done their GCSEs,” he says, although he remembers two or three who left before finishing their GCSE courses. “One of them left before she was 16 but apparently she kept up her education on the boat.

“When they get back to England [for holidays] they reconnect to Facebook and start updating their profiles but when they are over there at Sea Org they can’t update their profiles at all.”

On returning to the school for a play, a year after going to Florida, Fred says a few of the Sea Org students were “very different”.

“A few of them visited for a few days, and as they were my friends I hung out with them quite a lot, and they were really different, unpleasantly so. They were much quieter, they talked in a different way, in a slightly unpleasant way. They were less ‘there’. It was a very unpleasant experience meeting them again.”

How had they changed? “They were more like their parents. They were less open with me and less willing to discuss things with me, and this is what I heard from a lot of people.”

Alarmingly, many of the teenagers returning from Sea Org come back with husbands and wives.

“Almost all of those who came back from Sea Org had got married there or in the intervening period,” says Fred. “Some of them updated their Facebook with photos of their weddings. One of their mothers told me about how their daughter had been married.” Fred was “very surprised” to see his teenage friends getting married so young.

James, 17, a current student at the school whose parents are Scientologists but who calls himself an agnostic, says that on average three students leave for Sea Org each year. “A couple of my friends got married out of the blue. But you know, once they left school I didn’t really stay in contact.” He says both weddings happened within a year of their departure. One friend married a girl he was already in a relationship with at Greenfields. He didn’t recognise the other friend’s bride when he saw the photos.

“I’ve heard,” says James “and these are just rumours, that having relationships [at Sea Org] was strictly forbidden unless it was serious. I think that might have led some of the couples to getting married, so they can continue their serious relationship. I’ve heard it from a few people”.

When fellow pupils find out which of their peers has been chosen to go to Sea Org, it affects how they are treated in the classroom, according to another ex-pupil, Zach: “They are excited before they go, they are completely thrilled. And they get treated differently at school.”

They are “very tight-lipped about it”, he recalls, and “even quieter” around non-Scientologists. “If you asked, they would just walk away,” he said, “Even the regular Scientologists are kept in the dark about it.”

All of the ex-students who spoke to the Standard said that Greenfields is welcoming to non-Scientologists. The Standard asked the school for a response, but it did not provide one.

Katie Holmes may have shepherded her six-year-old away from a future with Scientology’s elite but a clutch of British families in the Sussex countryside seem less concerned about Sea Org, and the young marriage, behavioural change and alleged abuses that it apparently visits upon its teenage initiates.

*Some names and details have been changed.