New reports claim that Katie Holmes’s fears that daughter Suri was set to be inducted into a hardcore Scientology organization were the driving force behind the end of her marriage to Tom Cruise.

Katie Holmes, 33, was allegedly convinced husband Tom Cruise was planning to send Suri, 6, away to Sea Organisation – an association of Scientologists established in 1968 by L. Ron Hubbard, the science fiction writer and founder of Scientology.

Sea Org, as it is known, is where the highest levels of Scientology are taught and children as young as five can be sent to live there – without their parents.

The company has been often compared to a boot camp and several ex-Scientologists (including Oscar winner Paul Haggis) have been outspoken against its military-like conditions.

Initially created at sea, maritime customs and traditions persist today even in the land-based branches of the organization.

It claims to act as goodwill representatives and administrators of Scientology with the stated purpose to “get ethics in on the planet”. And a source told website TMZ that Tom Cruise is a big fan.

The website claims that Katie Holmes and Tom Cruise had been arguing over Suri’s indoctrination into Scientology – and it seems that for Katie talk of her six-year-old joining Sea Org was the final straw.

The huge Scientology boat The Freewinds that was the location of Tom Cruise’s infamous birthday party in 2004, is entirely staffed by Sea Org members and the highest levels of Scientology are taught on the ship.

According to the official Scientology website, members of Sea Org sign “a one-billion-year pledge to symbolize their eternal commitment to the religion and it is still signed by all members today”.

When Katie Holmes and Tom Cruise first got together in 2005, a prominent Scientologist who had been with the Sea Org since 1994 Jessica Rodriguez was transferred and became Katie’s assistant/Scientology chaperone.

Feshbach, in one of Katie Holmes’ first interviews after getting together with Tom Cruise, was described by a writer for W magazine as “cold-eyed” and “a third-wheel”.

Katie Holmes felt the only way to save Suri from being shipped off to Sea Org was to file for divorce and seek sole legal custody.

Tom Cruise’s devotion to the shadowy church of Scientology is set to come under scrutiny as, according to New York legal sources, his religious beliefs will be central in the divorce battle.

“There is no way her advisers will not be putting Scientology at the very core of this divorce,” says Mike Paul, a prominent New York crisis manager who counsels celebrities on how to handle high-profile court cases.

The heart of the divorce is nothing less than the battle for the soul of Tom Cruise and Katie Holmes’ daughter Suri.

Katie Holmes's fears that daughter Suri was set to be inducted into a hardcore Scientology organization were the driving force behind the end of her marriage to Tom Cruise

“The only possible reason for Katie to push for this is that she fears for the emotional wellbeing of her daughter,” says Mike Paul.

“Suri is at an age where she will be becoming more and more involved with the church and Katie clearly wants to make the break before her daughter is dragged into Scientology.”

In fact, Suri is understood to have been enrolled in Scientology-based school programmes by her father, which is said to “terrify” Katie Holmes.

Tom Cruise’s desire to immerse his daughter in Scientology is believed to have brought about a culture clash of religions with Katie Holmes, who was raised a devout Roman Catholic.

Indeed, such is the actress’s concern over a backlash from the sect that she is convinced rogue elements from the church have been monitoring her movements.

On Tuesday, a worried Katie Holmes called police to the New York apartment where she is living with Suri after spotting two mysterious men in a black Mercedes SUV parked outside the door.

Katie Holmes, who looks strained and gaunt, was said to be convinced they were not members of the paparazzi who sell footage of her and her daughter to American celebrity websites, but Scientology operatives. Apparently, neither had a camera.

According to celebrity website TMZ, Katie Holmes also believes she has been followed when she leaves the apartment in the fashionable East Village district.

In addition to the Mercedes, a white Cadillac has also been spotted regularly outside the apartment.

Meanwhile, others who have quit the church of Scientology say it goes out of its way to discredit and intimidate former members.

Sam Domingo, 45, a British mother of three who was married to the son of opera star Placido Domingo, says her life was made hell when she split from her husband and left Scientology three years ago.

“They are ruthless and quite happy to wreck families,” says Sam Domingo, who joined the cult at 21.

“My former husband was told to disconnect from me – cut me out of his life completely – and to contact our children only through a lawyer.

“For married couples thinking of splitting up, they make you confess all the things you have done wrong to each other. It’s incredibly intense and personal. But when I left they made public the information they had got on me and my husband.”

Meanwhile, there is increasing evidence that far from disintegrating only recently, the Cruises’ marriage has been at best semi-detached for at least three years.

While Tom cruise has remained at the family’s home in Beverly Hills when he is not filming, Katie Holmes has spent much of her time since 2009 on the opposite side of America.

Katie Holmes has been buying up other apartments in the 11-storey Manhattan apartment block where Tom Cruise has owned a flat since 1985 to enable her to build a gym and quarters for her security staff.

Katie Holmes has also enrolled Suri in a Catholic school in the city and is said to have removed all of her belongings from their Los Angeles home.

This makes something of a mockery of the increasingly hollow protestations that all was well in the marriage – not to mention those awkward hand-holding pictures of the couple taken just two weeks ago in Iceland where Tom Cruise is filming the action movie Oblivion.

The fact she has chosen to remain in New York is significant, not least because its courts tend to order children to remain with one parent in custody disputes, while those in California favor joint custody.

But Katie Holmes’ supporters say she has also felt it necessary to distance herself – and, crucially, Suri – from Scientology and members of the Cruise clan who are as devoted as he is to its strange teachings.

Increasingly, Suri is reaching the age when children from Scientology families begin their indoctrination process, which involves “auditing” – being connected to a crude lie detector called an e-meter and having to tell your deepest and darkest secrets to sect staff.

One of the principle reasons behind the split, say Katie Holmes’s circle, has been her growing skepticism towards Scientology, which was founded by Fifties sci-fi writer L. Ron Hubbard, who taught his disciples that humans are descended from space aliens called Thetans.

The couple had a lavish Scientology wedding in Rome in November 2006 at which the church’s leader David Miscavige was Tom Cruise’s best man – he was even said to have accompanied the couple on honeymoon.

Six months earlier, Katie Holmes had given birth to Suri amid rumors she had gone through a “silent birth” (Scientologists insist mothers should not scream or shout out in pain during labor in order for babies to be born in a calm environment).

And for anyone who imagines such tales are merely colorful myths, Kelly Preston, the wife of fellow celebrity Scientologist John Travolta, publicly admits she went through a silent birth with their son Benjamin in 2010.

But within a year of Tom Cruise and Katie Holmes’ wedding, which had received the blessing of the church’s hierarchy, the marriage was in trouble, with Katie having doubts about the sect’s all-consuming influence over her life.

In 2007, Katie Holmes stood up for herself and insisted on sacking her Scientology-hired “spiritual minder” Jessica Rodriguez, who was tasked with accompanying the actress 24 hours a day, seven days a week, and sitting in on interviews she gave about her marriage.

Even so, one former Scientologist, who was employed at its head- quarters in Clearwater, Florida, said that around the same time David Miscavige persuaded Katie Holmes to attend a Scientology boot camp at the organization’s Gold Base centre in Hemet, California, which is used for those having doubts about their faith.

At the 700-acre property, disciples are expected to exist on little food or sleep and detox by drinking vinegar mixed with calcium and magnesium.

They are also required to go through intense “auditing” sessions. The process is supposed to clear the mind of “engrams”, the Scientology term for painful experiences that block spiritual growth.

But throughout the marriage, Tom Cruise’s attempts to persuade his much younger wife to submit fully to the teachings of the church have met with resistance.

In 2008, two of the most influential figures in Tom Cruise’s circle, his mother Mary Lee and sister Cass – both devout Scientologists – mysteriously moved out of Cruise’s sprawling LA compound.

Tom Cruise put them up temporarily in an apartment at a Scientology-owned building on Hollywood Boulevard, which he largely funded through donations totalling millions of dollars.

At the time, Tom Cruise’s PR team insisted Katie Holmes had not thrown them out, but rumors were already rife that tensions with her in-laws had reached breaking point.

Likewise, reliable sources in the U.S. were privately speaking of tensions between Tom Cruise and Katie Holmes’ Catholic mother Kathy and lawyer father Martin, from whom she is said to have sought advice over the divorce.

Increasingly, the salons of Beverly Hills and Bel Air have been full of talk of Tom Cruise’s controlling ways, which are said to have extended to authorizing acting roles for Katie Holmes – who found fame in the TV series Dawson’s Creek – as well as his insistence she should remain pale-skinned, like his second wife Nicole Kidman.

And the couple spent ever longer apart, though officially it was claimed she had begun spending time in Manhattan only for work after appearing in the Arthur Miller play All My Sons on Broadway in 2008.

Throughout, Tom Cruise – who is 50 tomorrow – has publicly done his best to paint an unlikely picture of domestic bliss. As recently as two weeks ago, he was gushing about how lucky he was to be married, speaking at a Friars Club awards ceremony at the Waldorf Astoria in New York.

Significantly, however, while Suri accompanied her father to the event on one of his infrequent trips to New York, Katie Holmes chose to be nearly 7,000 miles away on business in Beijing.

Tom Cruise had seen his career dip temporarily in the embarrassing wake of his “jumping on the couch” moment, when he excitedly hopped up and down on a TV sofa professing his love for Katie Holmes, his then girlfriend, while being interviewed by Oprah Winfrey in 2005.

But he has spent much of the last two years on location in such far-flung places as Dubai, Vancouver and Cadiz shooting the movies Mission Impossible: Ghost Protocol, and Knight And Day with Cameron Diaz.

Quietly, Tom Cruise’s family, particularly his sister Cass – who home-schooled Isabella, 19, and 17-year-old Connor, the children the actor adopted with Nicole Kidman – have begun, say U.S. sources, to exert a greater influence on the upbringing of Suri during the time she spends with her father.

Nicole Kidman has blamed their children’s induction into Scientology for her long-distance relationship with them following her divorce from Tom in 2001. Clearly Katie Holmes does not plan on suffering the same fate with Suri.

An indication that Katie Holmes is prepared to play hardball from the outset comes in the guise of the colorful Allan Mayefsky.

The 58-year-old Harvard graduate was one of the principle legal players in the messy divorce of model and actress Christie Brinkley and her husband Peter Cook, which has become notorious as one of the most bitter of Hollywood break-ups.

New York-based Allan Mayefsky is a shrewd operator who has a habit of airing the grievances of his clients in front of the media.

He is known for demanding an even split of proceeds in divorces and for winning $45 million for the wife of a Wall Street financier in a landmark case in 2003.

Katie Holmes’ legal team also includes Jonathan Wolfe, a partner in the relatively low-profile firm of Skoloff & Wolfe, based in unfashionable New Jersey.

Crucially, Jonathan Wolfe is an expert in what is euphemistically known in American legal circles as “business evaluation” (in plain English, that means he is a terrier when it comes to finding hidden money).

Already specialist forensic accountants, employed by one of the two legal firms she has engaged, are busy untangling the complex web of businesses and trusts that manage Tom Cruise’s estimated $280 million fortune.

They want to establish Tom Cruise’s exact wealth, which suggests Katie Holmes is not prepared to walk away with the relatively modest settlement of $16 million that has been widely quoted – $3 million for every year of their five-year marriage as stipulated in the couple’s 100-page pre-nuptial agreement.