Tom Cruise: The subject of a less-than-flattering Vanity Fair piece. (Ian Gavan/Getty Images)

Tom Cruise skated mostly unscathed through what could have been a nasty PR debacle of a divorce from wife Katie Holmes. The split was finalized with no dirt spilled. Issues over child custody were quickly and quietly resolved. All lips, and legal documents, remained largely sealed. Cruise returned to his usual routine, one that involved taking daughter Suri Cruise to Disney World, making movies and preparing to promote his work in the upcoming “Jack Reacher.”

Now along comes what could be a bombshell of an article on the cover of October’s Vanity Fair, one whose headline declares “What Katie Didn’t Know: Marriage, Scientology Style.” The story — which has not been released in full but was teased online by the magazine over the weekend — goes into great detail about Iranian-born actress Nazanin Boniadi, a now-former Scientologist who, according to the story, auditioned to be Cruise’s wife, was his girlfriend from November 2004 to January 2005 and was ultimately deemed unsuitable as a partner for Cruise. After their break-up — again, according to the story — she was punished for revealing their relationship to a fellow Scientologist by being forced to do manual labor and sell copies of L. Ron Hubbard’s “Dianetics” on the street.

Scientology representatives have denied these details and dismissed the story’s sources as disgruntled former members of the church, Vanity Fair notes. Regardless, this seems like the beginning of another potentially damaging chapter in Cruise’s attempt to maintain his status as Hollywood’s most bankable and beloved leading man.

Based on what Vanity Fair has leaked, a lot of these details — the notion that Cruise would vet his potential romantic partners in such a clinical manner, or that fellow Scientologists would be so involved in that process — are not particularly surprising, especially to the Celebritologists who have been discussing such rumors in the comments section of this blog and others for years.

What is striking is that all this unsavory coverage is appearing in Vanity Fair, the same magazine that six years ago at this time, in its October 2006 issue, ran much-hyped, Annie Liebovitz-snapped images of a happy Cruise and Holmes with new baby Suri.

Cruise’s rep has tried to downplay the magazine’s shift in its approach to Cruise coverage, telling ABC News in a statement: “Lies in a different font are still lies — designed to sell magazines.”

Still, it’s not like Vanity Fair assigned this story to a reporter fresh off a summer internship with Hollywood Life. Maureen Orth, a longtime contributor to Vanity Fair and the widow of Tim Russert, presumably did her homework before writing the piece and suggesting that the magazine should run with it.

What’s more, director Paul Haggis — a former member of the church whose rejection of Scientology was documented last year in the New Yorker — has sent a lengthy e-mail to Showbiz 411’s Roger Friedman that corroborates Orth’s assertions about Boniadi.

Haggis’s statement reads, in part: “Naz was embarrassed by her unwitting involvement in this incident and never wanted it to come out, so I kept silent. However I was deeply disturbed by how the highest ranking members of a church could so easily justify using one of their members; how they so callously punished her and then so effectively silenced her when it was done.  It wasn’t just the threats; they actually made her feel ashamed, when all she had been was human and trusting ... She is not only a terrific actress at the beginning of a very promising career, she is a dedicated human rights activist and a truly lovely and caring person. The last thing she wanted or needed is this kind of publicity, but here it is, and I am sure she will deal with it with the same grace and dignity she exudes in her daily life.”

If the Vanity Fair story continues to build traction, and it seems likely that it will, Tom Cruise may be forced to personally respond to all this in some fashion. It seems unlikely that this one article will bring his career to a screeching halt, but still — to keep silent in the face of such unflattering details about him and his church may be too much for his reputation to bear.

As an international box office draw, Cruise still has juice, though clearly his track record has faltered a bit since his couch-jumping days. The people who enjoy seeing his uber-quick running and wide, handsome smile on a big screen will likely continue to do so without much regard for his personal life, unless something truly jaw-dropping is revealed.

But those who already see Cruise as, to borrow from this Guardian headline, the “biggest kook in entertainment” will undoubtedly have a field day with all this. The question now — aside from what other nuggets are nestled in Orth’s full-length piece — is how that field day will impact Cruise as well as Boniadi, the girlfriend that, until now, most of us never knew he had.