Tom Cruise, 43, has had a very difficult year. Although he has long had to contend with public scepticism about his Scientology beliefs, the state of his marriages, and allegations that he is homosexual – something he strenuously denies – the current media storm is more intense than ever, and is fuelled largely by his own missteps.

It began last spring with his very public selection of the actress Katie Holmes, 27, to be his next bride, an arrangement that some deemed more calculated than sincere. He followed that with a bizarre appearance on The Oprah Winfrey Show, in which he used Winfrey’s sofa as a trampoline, literally jumping for joy while shouting his love for Miss Holmes.

Next, he publicly reproached the actress Brooke Shields for taking antidepressants for postnatal depression. Two weeks later, he ranted against medically prescribed drugs and psychiatry on NBC’s Today programme. “I’ve never agreed with psychiatry,” he said. “It’s a pseudo-science.” It was an absurd statement. He also lost his cool when someone in a premiere crowd squirted a water pistol in his face. Most recently, Cruise and Scientology were the subjects of a hilariously disdainful send-up on South Park. The scheduled replay of the episode, Trapped in the Closet, was cancelled, allegedly to placate Scientologists incensed by cartoon mockery. Viacom, the New York media conglomerate that owns the company that makes South Park, also owns Paramount Pictures, the studio releasing Cruise’s next film, Mission: Impossible III.

Cruise, like the studios that release his films, now appears to realise the damage that has recently been done to his public image, and has changed the people who look after it. Gone is his sister Lee Ann, a devout Scientologist who, acting as his personal flack, closely managed his media contacts. She placed strict restrictions on access to Cruise, imposing peculiarly unique conditions, such as Scientology tours prior to interviews. Those interviews would be policed by her and allegedly taped so she could check for minor discrepancies in the ensuing articles.

In her place, Cruise has hired Rogers & Cowan, one of Hollywood’s most respected PR firms. When I interviewed Cruise in California, there were no restrictions – and the private person I met was very different from the man the public has come to know. We met in LA, where he shares a home with his younger sister, Cass, her three children, and his pregnant fiancée, Holmes, who was getting ready for the birth of their first child. He also has a third sister, Marian.

Normally guarded and defensive about his personal life, Cruise was surprisingly open and responsive when we spent an afternoon talking. He dropped his exuberantly self-satisfied public persona and allowed me to glimpse something of the fearful, troubled boy he had once been. It is that boy who governs the man Cruise has become. “I had no close friend, someone who understands you,” he said. “I was always the new kid with the wrong shoes, the wrong accent.

Cruise, born Thomas Cruise Mapother IV in Syracuse, New York, grew up in near-poverty in a Catholic family dominated by an abusive father he described to me as “a merchant of chaos”. His father was an itinerant electrical engineer who could never hold down a job and kept the family on the move in a restless search for work in the northeastern and Midwest United States, and Canada. His mother, Mary Lee, now 69, struggled to support the family.

“He was a bully and a coward,” Cruise said of the father who beat him. “He was the kind of person where, if something goes wrong, they kick you. He was an antisocial personality, inconsistent, unpredictable. It was a great lesson in my life – how he’d lull you in, make you feel safe, and then, bang! For me, it was like, ‘There’s something wrong with this guy. Don’t trust him. Be careful around him.’ There’s that anxiety.”

As a boy, Cruise said he was unable to read. Being in remedial classes away from “normal” kids caused him intense frustration. He felt excluded. It angered him. Small for his age, always the new boy, unpopular and lonely, he was eager to be liked and included. Instead, he was bullied regularly in the 15 different schools he attended in 12 years. “So many times the big bully comes up, pushes me,” he said. “Your heart’s pounding, you sweat, you feel like you’re going to vomit. I’m not the biggest guy, I never liked hitting someone, but I know if I don’t hit that guy hard he’s going to pick on me all year. I go, ‘You better fight.’ I just laid it down. I don’t like bullies.”

When Cruise was seven, his reading disability was diagnosed. “The school took me to a psychiatrist to get tested,” he recalled.

“They said, ‘Oh, he’s dyslexic.’ I’m labelled. It instantly put me into confusion. It was an absolute affront to my dignity.”

The diagnosis created the emotional basis for his contempt for psychiatry.

“I remember thinking, ‘I’ve got to figure this out. What’s normal? Am I normal? Who’s to say what’s normal?’ When I was growing up there was the whole civil-rights movement and I’d see people on the news going, ‘Well, of course, the black isn’t normal.’ I remember going, ‘What are you talking about?’ I didn’t understand what ‘normal’ is. It still doesn’t make sense. This is what led me to the study of psychiatry. I went and looked at it and realised all these labels don’t mean anything. Labels aren’t a solution.