One of the more interesting theories surrounding the film is that it was all an elaborate, expensive way for Kubrick to toy with the psyche of Tom Cruise. The details of the shoot certainly add weight to the theory, and the below facts, if recounted about any other combination of people, would sound like the work of a power-crazed tyrant and a hapless victim. Here, we explore the ways in which Kubrick beautifully messed with Cruise
From Tom Cruise: An Unauthorized Biography by Andrew Morton
"While Kubrick encouraged the couple to come up with their own ideas for scenes, he seemed to indulge Nicole far more than Tom, jotting down her ad-libs and accepting her choice of music, Chris Isaak's "Baby Did a Bad Bad Thing," for a sex scene between them. He described Nicole as a "thoroughbred" and Tom as a "roller coaster."
There remained the suspicion that, for all the mutual admiration, there was an element of humiliation involved in Kubrick's treatment of Tom. While Frederic Raphael recognizes but does not endorse the argument, he concedes that for Kubrick "breaking people and feeding them into his machine was maybe a reflex he could not resist." When Kubrick was rewriting the script, he would often fax Tom pages in the middle of the night, ensuring that his leading man was living his life according to the director's body clock.
Or when Kubrick filmed a scene in which Tom's character was knocked to the ground by a gang of drunken college louts who accused him of being gay, was this a wink to the audience being aware of the rumors circulating about the actor? Even Raphael is not sure, noting that in the novel the chanting youths accuse the doctor of being Jewish. It was Kubrick who changed the insult.
This ambiguous relationship played out most explicitly when Kubrick filmed the sex scenes involving Nicole and her navy lover. Noticeably, the six-day shoot was the only time in the marathon production that Tom was definitely not needed on set. Not so his scriptwriter. In a knowing aside, Kubrick told Raphael that Nicole had agreed to take off her clothes and he would be filming on a closed set for the next few days. "Might be a good day to happen to drop by the studio, if you wanted to," he told him. Raphael declined, feeling that it would be "cheap" to take advantage of the situation