The men who came for Marty Rathbun wore a kind of uniform: dark glasses, clipped facial hair, and light blue T-shirts. Each carried either a microphone, or a video camera. On their chests were pictures of a squirrel, upon which a photograph of Marty's head had been crudely superimposed. Topping off the ensemble were black baseball caps with an embroidered slogan stitched in white above the peak. It proclaimed: 'SQUIRREL BUSTERS'.

There were four of them, and they appeared around lunchtime on 18 April last year. Marty was making a sandwich in the kitchen of his home in Ingleside on the Bay, on the Gulf Coast of Texas. When he heard them knock, he grabbed a video camera kept on his sideboard for such an occasion. Then he turned it on to 'record' and proceeded to the front door.

There followed a brief altercation which, even by the standards of YouTube, where clips of what occurred were later posted, seems impossibly surreal. "Come on, Marty!" bellows the group's middle-aged leader, who wears a camera on his head, "got anything to say?" Rathbun asks who he is. "I'm with Squirrel Buster Productions," comes the reply. "I'm doing an investigation on you, and your squirrel technology." Heated discussions ensue. "We'll be here for weeks and weeks," promises one of the men, after Marty orders them off his property. Another adds: "As long as it takes!".

They weren't lying. From that point onwards, men wearing 'squirrel buster' outfits began turning up outside Rathbun's home every few hours. Sometimes, they'd arrive in a car; often, as the long, hot summer wore on, in a golf buggy. Occasionally, they moored boats in the canal outside his home. According to a harassment log local police advised Marty to keep, they'd video him inside and outside the property. From time to time, they'd also pepper his wife, Monique, with hostile questions, often about their sex life.

The 'squirrel busters' stayed in Ingleside throughout May, June, July, and August 2011. They rented homes nearby, carried placards denouncing Marty, and posted occasional footage of him on the internet. Soon, they became the talk of the village. One day, as news spread, Mark Collette, a reporter from the Corpus Christi Caller, appeared on Marty's doorstep and asked what was going on. The answer left him stunned.

Here, in this seaside hamlet, full of retirees and fishermen, Marty Rathbun was fighting an extraordinary religious war. The 'squirrel busters' were among its (possibly self-appointed) foot soldiers. At stake in the dispute, which has now been running for almost three years, is the future of one of the world's most controversial and headline-prone spiritual institutions: the Church of Scientology.

A few weeks ago, I travelled to Ingleside to meet Marty Rathbun, who is 55 and shares his home with Monique, a lapdog called Chiquita, and several hundred books by L Ron Hubbard, the science-fiction author who founded Scientology in the 1950s. Like many people drawn to the faith, he is an easy conversationalist with a fascinating, if somewhat troubled life story. We started from the top, and ended up talking for a little more than three hours.

Many aspects of Marty's story are disputed by the Church, which calls him a liar, a criminal, and an apostate. But the verifiable facts are as follows: he was a fully-paid-up Scientologist for 27 years, before quitting in 2004. For much of this time, he was a high-ranking executive in the Church, helping steer some of its most sensitive legal campaigns. He was also acquainted with many celebrity members, including Kirstie Alley, John Travolta, and Tom Cruise.

Marty says he left the Church for two reasons. The first is what he calls the increasingly onerous financial demands it places on followers. The second is a series of personal disagreements with its leader David Miscavige, a charismatic former associate of Hubbard who has reigned over Scientology since the mid-1980s. Over the years, Miscavige has built ties to a string of Hollywood personalities. When Cruise married Katie Holmes in 2006, he was best man.

When Marty left, eight years ago, he dropped off the radar and attempted to build a completely new life. But in 2009, after renewing contact with a handful of disaffected former colleagues, he changed course. First, he launched a blog, which has become a popular forum for the Church's critics. Then he turned his home into what he calls a "half-way house", offering refuge to people attempting to leave Scientology.

Since then, Rathbun has provided a temporary home to 72 defectors. His blog, 'Moving on Up a Little Higher', gets around 10,000 hits a day. It has been visited a total of six million times, is credited with encouraging scores of former Scientologists to quit, and has broken a string of sensational news stories about the Church, including film director Paul Haggis's resignation, in 2010, and January's decision by Debbie Cook, a senior member of Church clergy, to quit in protest at what she called its "extreme" fundraising. Almost every former Scientologist I have spoken with checks it daily.

Today, Marty has become one of the Church's most public detractors, and has appeared in that guise on virtually every major US news network. Tony Ortega, the Village Voice editor and one of the most prolific journalists covering Scientology today, wrote recently: "There may be no greater outside threat to the continued existence of the Church of Scientology than a lone man who lives near Corpus Christi and who operates a blog he updates about once a day".

I spoke to several ex-Scientologists who have stayed with Rathbun. "When I left Scientology, I lost every friend I had," said Samantha Domingo, who quit in 2009, after 20 years. "Then I went to see Marty. He gave me certainty, gave me hope, and made me realise I wasn't alone." Domingo, the British former daughter-in-law of the opera great Placido, now lives happily in Kent. "He picked up the broken pieces of my life and put them back together," she said.

John Brosseau, who quit the Church in April 2010, after 30 years, recalled: "Leaving felt like jumping out of an aeroplane with no parachute. But after two weeks at Marty's place I got my feet back under me. He put me in touch with a community of former Church members. One even offered me a job. It's been two years since then; I've now got a home, a wife, and a wonderful six-month-old daughter."

Marty does not charge house-guests. But he does accept their financial donations. Along with financial pledges to his website, these now represent his entire income. Critics say he is therefore leveraging his former status within the Church for financial gain. In a letter sent in 2009, Tom Cruise's lawyer, Bertram Fields, asked Marty to stop using his blog to mention the fact that he was the actor's former counsellor. "This is... a serious invasion of Tom's privacy and a violation of the priest-penitent relationship," wrote Fields. Rathbun replied, insisting otherwise. Cruise did not pursue the claim.

In March, I contacted the Church's PR department to inform them that I was writing a profile of Marty, and asking if they would like to respond to criticisms he had made of them. I also sought to check a few points of fact. They asked me to submit questions via e-mail. A few days later, their response arrived. It covered 15 pages. A second letter arrived at The Independent's offices in London the following day, from the Church's British lawyers, Carter-Ruck.

The Church called Rathbun "an anti-Scientologist, desperate and delusional". It said he was "expelled from the Church for violating Scripture" and has "a history of malfeasance" recently exposed in detail by Freedom, Scientology's in-house magazine, which claims he belongs to a "posse of lunatics". It advised me to research Marty via the website whoismartyrathbun.com. Among other things, it dubs him a "cult militia leader" and claims, "Rathbun's eyes glow with a psychotic gleam".

Since Scientologists "live in the community", the Church's letter argued that "the idea of a half-way house is absurd". It said Marty had been responsible for "lies, obstruction of justice, and violent behaviour" within the Church and had been dismissed from an executive position in the organisation rather than having, as he claims, quit. Because of his work since then, it claimed: "he is what we call a squirrel (a heretic)".

All of which brings us back to the strange campaign that began in Ingleside on the Bay last year. If, in the argot of Scientology, Marty is indeed a "squirrel", it follows that the cameramen who turned up at his home were out to "bust" him. Regardless of where they came from (and the Church formally denied being behind their activities), Marty came to the view that these strange men, with their golf buggies, weird T-shirts, and highly-visible surveillance equipment, had a plan: they wanted to shut him down.

To properly comprehend the threat Marty poses to the Church of Scientology, you need to grasp an important point: though no longer a Church member, he has by no means renounced the faith. Instead, he calls himself an "independent" Scientologist.

In practice, this means Marty still subscribes to many key tenets of the religion. He continues to practice "auditing", the form of counselling Scientologists use to seek enlightenment, and he continues to revere Hubbard, whose books and lectures he frequently quotes. Like L Ron, he believes firmly in reincarnation. "The way I see it," he told me, "this faith has a lot in common with Zen Buddhism."

Marty insists, however, that the Church, which he calls "corporate Scientology", has become estranged from its core values. In recent years, he argues, an organisation created to harness individualism became obsessed with loyalty, discipline and control, with getting members to obey rules, and, above all, with separating them from their money. "I never doubt the gains that I got from Scientology," he says. "I've never doubted the effectiveness of auditing. But I believe there's a real problem with the Church. The core poison is greed. I look at Scientology, and I think it's being destroyed by this quest for the buck."

The Church, for its part, denies placing unreasonable financial demands on members, claiming that it's perfectly possible to participate in the faith without making financial donations, and pointing out that all religions depend on the financial support of members. In a statement, it added: "There are no such things as 'independent Scientologists'. Scientologists are members of the Church... Others are squirrels."

Either way, critics such as Tony Ortega believe Marty's reformist platform is central to his ability to win over disaffected Scientologists. "He speaks their language. He's not abandoned Hubbard. He's not given up on the faith. He's just worn down. And the people he's speaking to are also worn down. They are exhausted with requests for donations. Because of that, he reaches deep inside the organisation."

In the eyes of supporters, Marty is not even an enemy of Scientology. Instead, he is leading a sort of Reformation. "Marty presents himself as a true believer," says Janet Reitman, the author of Inside Scientology, perhaps the most complete history of the Church. "He still believes in the faith, but he's trying to reform it. He sees himself as a Martin Luther figure."

Marty argues that "corporate Scientology" is dominated by fundamentalists who mandate literalist readings of its theological texts, including a famous piece of literature by Hubbard which argues that mankind's problems are the work of a despotic alien called Xenu who fought an intergalactic war 75 million years ago (see box). Marty would prefer to see that story as allegorical, in the same way many Christians view the Old Testament. The Church counters: "This shows he is no longer a Scientologist. Scientologists are true to the writings of Mr Hubbard".

Marty is also sceptical about the Church's rigid system of self-advancement, which requires members who wish to ascend its 'Bridge to Total Freedom' (see box) to take paid study courses. "There's an old rumour, from the 1970s, that Yvonne Jentzsch, who founded the Church's Celebrity Centre, tried to convert Led Zeppelin," he says. "The band got the sales pitch, and didn't buy, but later wrote "Stairway to Heaven" about Scientology. If that's true – and I'm not saying it is – I'd have to agree with Led Zeppelin. Scientology has become a stairway to heaven."

Marty's views strike a chord with many Church members who are struggling with their faith. I recently spoke with Luis Garcia, who had been in Scientology for 28 years, ascending to OT8 (the highest level of The Bridge) before stumbling on Marty's blog in 2010. "Reading it had a therapeutic effect," he said. "It made me realise that I wasn't the only one with doubts. He reflected exactly what I was thinking."

I also spoke with Mike Rinder. He was one of the Church's most senior executives, working in its PR department, before leaving in 2007. "Marty's blog is a forum for information," he said. "That's what makes it such a threat. He's not trying to be a leader of men, or take over the Church, or storm the castle walls. He's just a guy on the outside who wants to speak his mind."

Their experiences illustrate a fundamental truth about the Church's future in the internet era. Unlike during previous decades, when defectors had no means to communicate with each other, today's breed can join forces and make themselves heard. "There have been exoduses of senior staff in the past, but they haven't websites like Marty's to connect them," adds Reitman. "Now, for the first time, they have been able to build a significant resistance movement, which isn't going away."

The web makes it impossible for anyone to silence critics. Typing 'Scientology' and 'cult' into Google will return more than three million hits. Searches for 'Scientology' on YouTube will turn up a wealth of footage, most of it negative – from tapes of Tom Cruise jumping on sofas, to scatological clips from South Park, to two revelatory documentaries about the Church by the BBC's John Sweeney.

How deeply this affects recruitment is impossible to say. The Church insists that its membership is "estimated to be in the millions" (though academic studies have put it in the tens of thousands). But the sheer volume of critical material that now exists online can hardly attract new members.

"The internet is a curse for Scientology," Sweeney tells me. "In the old days, people thinking about quitting would have had to go to bookshops to hunt down scepticism. Now, one click takes you to Xenu... When they've picked themselves off the floor and stopped laughing, they may start wondering about the Church that likes to wear dark glasses."

Marty's journey in Scientology began on a pavement in Portland, Oregon. It was 1977, and he was walking to a bus stop when a man outside one of the Church's missions thrust a leaflet into his hand. "Look, man, I got 45 minutes to my bus," Marty told him. "Tell me what it is you're doing here." The man said he was seeking recruits for a three-week course that advanced "a technology for improving communication".

Marty, who was then aged 20, was a troubled soul. His mother had committed suicide when he was five, and his brother suffered from schizophrenia. He'd been brought up in bohemian Laguna Beach, California, and experimented with drugs as a teenager, before dropping out of college. "I was having serious problems with communication, so what the guy said intrigued me," he recalls. "The course was 50 bucks. I only had 25, but he said, 'If you pay cash, I can get you in'."

The next three weeks were "life-changing". Marty was given intensive auditing, carried out lengthy meditation exercises, and at one point during a "communication drill" in which he had to silently stare into a counsellor's eyes for an hour, underwent what he calls an "out-of-body" experience. "I literally exteriorised from my body," he says. "It was incredible. It changed everything."

A few weeks later, the Scientology mission in Portland was visited by a man from Los Angeles, wearing a quasi-naval uniform. He was a member of Sea Org, the Church's version of the clergy, seeking new recruits. "He was dynamic, and he spoke about working to change humanity. I was sold," says Marty. He duly joined Sea Org that day. Like every other member, he signed a billion-year contract.

I asked Marty how an outwardly normal 20-year-old could, in the space of a few short weeks, become so committed to a minority religion that he would agree to devote his entire life to it. "What you don't understand," he replied, "is how much of Scientology really works. The auditing, and the counselling, and the communication drills sorted me out. They completely changed me."

Members of Sea Org are given board, lodging, and a small allowance. They are also offered resources to further study Scientology. In return, they are expected to work for the Church, in whatever capacity they are asked. Marty was sent to Los Angeles, on a stipend of $17 a week. "It was kind of cool," he says. "I thought it was a great socialist experiment. I mean we all lived communally. We were people who shared the same ideas. I was engaged. You can't help but be engaged. It was a hive of activity."

At first, Marty performed fairly menial tasks. But over the years, his seniority grew. By the late 1980s, he had become a trusted lieutenant of David Miscavige, who had in turn inherited the leadership of the Church following the death of Hubbard in 1986. His remit included contributing to some of the Church's most important legal battles, and attempting to silence its critics.

In 1993, Scientology won a 30-year campaign to be granted exemption, as a religious institution, from US taxes. It was a huge moment: loss might have bankrupted the Church. In 1995, Rathbun led the Church's response to one of the greatest crises in its history: the death of Lisa McPherson, who had suffered a mental breakdown at Scientology's Flag headquarters in Florida, and died while in its care. The felony charges it faced were eventually dropped.

In the same era, Marty became adept at battling news organisations seeking to cover Church affairs. In the early 1990s, he helped pursue an epic defamation case over Time magazine's cover story, 'Scientology: the cult of greed'. The Church eventually dropped its claim, but not before Time Warner had endured five years of litigation.

Marty was also a gifted auditor. And by the end of the 1990s, he had worked with a slew of celebrity Scientologists. In 2001, Tom Cruise, who was going through a divorce from Nicole Kidman, asked him to come to Los Angeles for some sessions. "It was a big deal, because Tom hadn't been on line with the Church for eight years, and that had been a huge loss," Marty says. "So I went to LA and helped him."

Later that summer, Cruise asked Marty to help him "devote serious time" to Scientology. "From July to November 2001, between Vanilla Sky and The Last Samurai, he was with me almost every day. He was actually practising for Samurai between sessions. He had swords with him all the time."

Cruise had recently embarked on a relationship with Penelope Cruz. Marty says he was asked to recruit her to the faith. It didn't work. "She was doing auditing, and she was doing it with a very open mind, but she never really bought into it," he recalls. "She was a professed Buddhist, and she was continuing to meditate, and that ended up freaking people out."

Marty says he also audited Kirstie Alley, helped Lisa Marie Presley during her very public separation from Michael Jackson, and worked with John Travolta ("a very sweet guy; innocent and sometimes naïve, but sweet"). He also became close to Greta Van Susteren, the Fox News pundit and longstanding Scientologist, who quietly assisted Church PR campaigns near its Florida headquarters.

"Greta's very wary of wearing Scientology on her sleeve. But she had this yacht, the Sequoia. She'd bring it to Clearwater harbour when she came down for the holidays. Opinion leaders from the local community would be told, 'You're invited to have dinner with Greta on her yacht'. She'd be very charming, without ever talking about Scientology. Afterwards, guests would be informed: 'She's a leading Scientologist and as you can see, she's also a regular person'. It would really impress them."

I asked the Church about Marty's dealings with high-profile members. It responded: "the Church does not comment on spiritual advancement of any parishioners. This is shameless name-dropping by a defrocked Scientologist".

Marty's career in the Church came to an abrupt end on 12 December 2004. The reasons for his departure are hotly disputed. He claims to have witnessed troubling abuse at a Scientology compound in Riverside, California. Several other recent defectors who were there at the time have publicly supported that version of events. However, the Church describes their claims as "blatant fabrications" which reveal him to be "an apostate and anti-religious hate-monger". Either way, he fled on a motorcycle, and has not been back since.

It's hard not to conclude, taking a long view of Marty's 27 years in Scientology, that his role in the Church made him uniquely suited to his current life outside it. "Marty was the guy who used to be the Church's enforcer. So when they go after him, he has the full knowledge of what their tricks are," Tony Ortega told me. "I mean, when the squirrel busters came to his home, he just sucked it up. In fact, I got the impression that he was almost enjoying it."

The men in strange outfits stayed in Ingleside for several months last year. Their modus operandi became simple: they'd walk to the edge of Marty's property line, and film there. Any subsequent confrontation would then be captured on tape. "Their endgame," says Marty, "was to get me prosecuted for assault."

When newspapers asked the Church what was going on, they denied any affiliation with the squirrel busters. But regardless of who was pulling their strings, they got under Marty's skin. A total of 13 criminal complaints were filed against him, following various scuffles, though none resulted in a prosecution.

At one point, he came close to leaving town. "I went to the local council when it started getting pretty heated in May or June, and said, 'Look I'm the guy who dragged these horseflies in here, and I'm sorry and if it doesn't end, we're going to move house'," he says. But the locals were having none of it. "They said, 'You're not going anywhere!'," he recalls. "The lady who lives next door told us, 'This country was founded on freedom of religion. Who are they to come across the country and tell you how to go about your religious activity? That's not America!'."

On 1 September, Marty recalls asking a squirrel buster called Norman James Moore to stop bothering his wife. When Moore didn't respond, Marty snatched the sunglasses from his head. On 18 September, a police car appeared at Marty's door and told him he that was being arrested. Mr Moore had filed an assault charge, claiming that his forehead had been scratched during the incident.

Four days later, local prosecutors made an announcement: no jury, they said, would possibly convict Rathbun after learning of the circumstances he had endured during the previous five months. All charges were dropped. "We took a totality of the circumstances," said a spokesman. "We examined the level of provocation and the extent of the injury, which was literally a scratch." The decision brought national media attention on Marty. Shortly afterwards, he was invited to discuss the affair on Good Morning America.

September 18th turned out to be the last day the squirrel busters ever appeared on Marty's doorstep. Maybe they had grown bored. Maybe their leaders realised that their presence was becoming counterproductive. They left town on 2 November, no less than 199 days after arriving. Since then, Marty has been blogging daily, running his "halfway house" and writing a memoir of his career in Scientology. He hopes to publish it later this year. "I've seen the Church from inside and out, over such a long period," he says. "It's made me realise that the best thing I can possibly do is to tell my story, warts and everything, and let people make up their own minds."

Scientology: a beginner's guide

Scientology posits that a form of counselling known as 'auditing' can allow human beings to identify pain experienced years ago. The process of confronting that pain will improve their emotional well-being. During sessions, subjects are questioned while attached to an 'e-meter', which measures resistance being exerted on an electrical current being passed through someone's body. Scientologists believe that both conscious and subconscious thoughts affect the e-meter's reading. By locating and dealing with their subject's harmful thoughts, an accomplished auditor aims to help them reach a state of enlightenment known as 'clear', where their negative sentiments have been wiped out.

Church members follow a study programme called 'The Bridge', or 'The Bridge to Total Freedom', based around texts and lectures created by L Ron Hubbard. It boasts dozens of different levels, which take years to complete.

The cost of ascending The Bridge is fiercely disputed. To complete each stage, members must pay for lengthy auditing sessions and intensive study courses. David S Touretzky, a professor at Carnegie Mellon University who has researched Scientology, says that, based on price lists he has analysed, the total cost of ascending to the highest level, OT8, runs to $500,000 (£315,000).

However the Church calls that figure 'absurd'. A spokesman said that ascending The Bridge involves an 'intensive amount of study, equivalent... to about two years of university study' but costs less than two years of tuition at a typical US university, such as UCLA.

At a stage called OT3, Scientologists are presented with L Ron Hubbard's creation theory, known as 'The Wall of Fire'. The Church refuses to publicly discuss this aspect of its theology, deeming it potentially harmful in the hands of anyone who has not been properly trained. But details entered the public domain in 1985, in documents released by a court in Los Angeles.

A summary of The Wall of Fire published by the LA Times reads: "A major cause of mankind's problems began 75 million years ago, when the planet Earth, then called Teegeeach, was part of a confederation of 90 planets under the leadership of a tyrannical ruler named Xenu. Then, as now, the materials state, the chief problem was overpopulation.

"Xenu decided to take radical measures to overcome the overpopulation problem. Beings were captured on Earth and on other planets and flown to at least 10 volcanoes on Earth." After that, "H-bombs far more powerful than any in existence today were dropped on these volcanoes, destroying the people but freeing their spirits – called thetans – which attached themselves to one another in clusters.