Inside Scientology: Is the church's controversial Sea Organization what drove Tom Cruise and Katie Holmes apart?

Following the news that Katie Holmes reportedly blindsided Tom Cruise by filing for divorce last week, the burning question is what went wrong between the couple, whose relationship at one time was so passionate that Cruise was literally jumping up and down on national television about it. Numerous reports link the split to Cruise's devotion to Scientology, stating that Holmes, 33, became concerned for the welfare of their 6-year-old daughter, Suri, as the girl's involvement with the controversial religion was set to increase. Holmes' divorce papers, seeking sole custody, spoke volumes.

According to TMZ, Holmes is divorcing Cruise in part because she believed he planned to send Suri away from home to a hardcore Scientology association known as Sea Organization. "Sea Org, as it is known, is where the highest levels of Scientology are taught and kids as young as five can be sent to live there ... without their parents — and our sources say Tom is a big fan," states the website. "The Sea Org 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."

The official Scientology website has a different description for the group, which it calls "the singularly most dedicated Scientologists," who "have committed their lives to the volunteer service of their religion." Established in 1967, the Sea Organization once operated from a number of ships, but today the majority of the 5,000 members are based on land — though they still "wear maritime-style uniforms and have ranks and ratings." The Scientology boat Freewinds — on which Cruise celebrated his 42nd birthday during a party that cost an estimated $300,000 — is operated by members of Sea Org.

[Related: Tom Cruise's three marriages: the rundown]

"As volunteers and members of a religious order, Sea Organization members work long hours and live communally with housing, meals, uniforms, medical and dental care, transport, and all expenses associated with their duties provided by the church," states the Scientology website. "They also receive an allowance to purchase personal items, as all of their other expenses are fully covered by the church." Minor children are permitted to voluntarily join with the consent of a parent and schooling is provided, but the children also work. However, the website emphasizes: "The Church of Scientology adheres to all child labor laws and no underage Sea Organization members are permitted to perform tasks or to work hours longer than permitted by law."

Although Scientologists deny there is any wrongdoing in relation to the group, there have been numerous reports stating that conditions for children within the organization — who, according to the Scientology website, are made to sign "a one-billion-year pledge to symbolize their eternal commitment to the religion" — are less than optimal. "Crash" screenwriter/director Haggis, who was a member of the church, has said that allegations of abuse of the children were partially behind the reason he left Scientology after 34 years. In a 26-page article in The New Yorker, he said he heard about horror stories from men and women who joined Sea Org before turning 18. “They were 10 years old, 12 years old, signing billion-year contracts — and their parents go along with this?” Haggis said. “Scrubbing pots, manual labor — that so deeply touched me. My God, it horrified me!” In the same article, a former employee claimed to have worked 15-hour days as a teenager, seeing her parents only two times between the ages of 12 and 18. Another said he earned $17 a week for his work, and resided in living quarters that were so lacking that his room didn't even have a door knob.

Outside of that, the website Ex-Scientology Kids, which was started by three women who had grown up in the church but later left, has a forum where many people share stories of mistreatment. Additionally, in 2010, a former Scientologist named Keryn (she didn't disclose her last name) went public with her story, claiming she was a "child slave" for Sea Org in the 1960s. Her mother was a high-ranking Scientologist and at the age of 12 Keryn started working on one of the church's ships, where the church's elite followers stay and study, before her grandmother helped her escape at the age of 13. "When we were on the ship, we had people working 20 hours a day, seven days a week," she told Australia's ABC News. "A lot of the children hadn't seen their parents for months, and their parents were on the same ship." She also alleges that she saw a 6-year-old boy chained up by the leg in a ship's hold for days. "He was fed, but he was chained," she said.

Even if Suri doesn't join the hardcore Sea Org, there are apparently concerns Holmes has about the religion in general, specifically "security checking," an interrogation process in which an ethics officer asks about 100 questions to children, starting at age 6. Questions range from "What has somebody told you not to tell?" to "Have you ever bullied a smaller child?" The Village Voice spoke with Marc Headley, who grew up in Scientology but left in 2005, about sec checking. "You get conditioned to tell them everything they want to know," he said. "It's all just information gathering." His wife, Claire, added: "I was sec checked when I was 7… I can think of numerous minors who received sec checking. It's probably more prominent in the Sea Org, but I don't think it was limited to the SO."

[Related: Suri Cruise: Six Years of Style (Photos)]

Our calls to a spokesperson for Scientology International were not returned.

Holmes is seeking sole legal custody and primary residential custody of Suri, a move that ensures she'll be able to make decisions on the girl's education and religion choices. At the time her divorce became public on June 29, her lawyer, Jonathan Wolfe, said in a statement that "Katie's primary concern remains, as it has always been, her daughter's best interest." The lawyer declined comment on this story.

When Cruise ended his marriage to Nicole Kidman, who like Holmes was raised Catholic, their two children continued down the road of Scientology with Isabella attending Delphian School, a boarding school in Oregon run by the church. Since her divorce, Kidman has rarely been seen with Bella or her son Connor and says very little about their upbringing. However, in 2007 Kidman revealed to the UK-edition of Marie Claire that the children opted to live with Cruise in Los Angeles. "When children are teenagers, they have a say in where they want to be," she said. As for their upbringing, "Yes, they're being raised as Scientologists," she said, adding: "I don't want to go there."

Rumor has it that Cruise will soon be filing his own divorce papers, seeking joint custody of Suri. For now, Cruise — whose lawyer said was "deeply saddened" by the divorce news (his lawyer didn't reply to a request for comment on this story) — is filming his thriller “Oblivion” in Iceland and getting ready for this 50th birthday on July 3. Meanwhile, Holmes seems to be regaining her independence. According to People, the actress has fired her soon-to-be ex-husband's security team and is living in a new apartment in New York City. The magazine also reports that earlier today, Holmes kept her previously scheduled appearance on the Lifetime reality fashion competition "Project Runway: All Stars.” She attended the taping at Parsons The New School of Design in Manhattan.

More Celebrity Features on Yahoo!:

Follow omg! on Twitter