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.

“I wanted to learn how to read. I was struggling, trying to get through class. When I’d read a page I’d go blank at the end of it. In class I’d be like, ‘Please don’t call on me. Please!’

Cruise claims he didn’t fully overcome his dyslexia until his twenties, when he learnt to use dictionaries. “No one teaches you about dictionaries. I didn’t know the meanings of lots of words.” Figuring out how to look up words in a dictionary is one of the “technologies” that Scientology offers its members.

In 1974, when he was 11, his parents divorced. After that, nothing was the same. “It was painful,” he said. “My mother finally had the courage to stand up to my dad and say, ‘No more! I’m not taking it. So long.’ People can create their own lives. I saw how my mother created hers and made it possible for us to survive. My mother was the one who rose to the occasion. She held three jobs. She said, ‘We’re going to get through this.’ And I decided that I’m going to create for myself who I am, not what other people say I should be. I’m entitled to that.”

Cruise’s mother packed up the family station wagon and drove her kids to her home town of Louisville, Kentucky.

“My dad didn’t leave,” he said. “My mother left my father.” Cruise, the second oldest child and only boy, was parcelled out to live for about a year with an aunt until his mother was able to establish the family together under one roof. Although the family received federal food stamps, they were ineligible for full welfare benefits because his mother worked. “My mother went to the welfare office and the guy said, ‘If you lose that job we can help you with finances,’” Cruise recalled. “My mom came home and said, ‘Okay, here’s the deal. To get more help from the government, I’d have to get rid of one job. I’m not going to do that.’

“My mom could have sat there every morning and cried and cried. She didn’t. My mom was very proud. She had dignity. She’s going to work hard. My mom had to pay the bills. She said, ‘What can I do to help my family? I’ve got to take care of my family. Maybe you kids don’t have as much as the guy next door, but what you have is going to be clean. You’re going to eat.’ Don’t make any mistake about it – it was a roller coaster. But there was a definite sense that we were going to be okay.”

The family received no paternal child support. “My father stopped working. He had a hard time, but his kids needed help. The breadwinner has to go out and get the bread so we have a roof over our heads and food. He didn’t do things to help his family or his friends or himself. He wasn’t the greatest father. But here’s the thing: I’m not him.”

At 12, Tom Cruise stopped using his dad’s last name. He did not see his father again for almost 10 years. “He was in the hospital dying of cancer, and he’d only meet me on the basis that I didn’t ask him about the past,” he said. “My father had contributed to the destruction of a family.”

His father never saw any of his son’s films, or apologised to him for his mistakes. “I was fine with it,” Cruise said. “When I saw him in pain I thought, ‘Wow, what a lonely life.’ He was in his late forties. It was sad.” His father died soon afterwards, in 1984.

In 1978 Cruise’s mother got married again, to John South, a plastics salesman. He was a step up for the family. Tom was 16. They moved from Kentucky to suburban Glen Ridge, New Jersey, near New York City. Cruise went away to a Catholic seminary in Cincinnati, Ohio, when he was a teenager, hoping to discover where he belonged. “I looked at the priesthood and said, ‘Listen, this is what I’m going to do. They [the Catholic Church] would pay for the boarding school for a year. I knew being there would help my family financially. The school also had hobby shops and remote-control boats and planes.

“I was interested in spirituality and the virtues of that. As I was growing up, my dad went from being Catholic to Episcopalian [Anglican] to being an atheist. It was Christianity throughout, and it was all over the place. I was very curious.

“I’ve always been greatly interested in life,” he continued. “When I was three or four, I’d get on my tricycle and take off by myself in the morning. My mom didn’t spank me for doing that. I loved exploring. I didn’t have any fear. I’d climb the tallest tree. I liked being on top with the wind blowing back and forth. To get me down, my mother didn’t go, ‘Come down! You’re going to kill yourself!’ She’d say, ‘Honey, how you doing?’ I’d look down. She was a speck. ‘Tommy, I’ve got a cake for you if you come down.’

He smiled as he remembered it. “So I was interested in life, asking lots of questions, like my own children do, wanting to know for myself. I remember being seven, lying in the front yard, looking at the clouds, going, ‘What is this all about?’ There has to be answers.”

Cruise, however, did not find them in the Franciscan seminary. “After a year, I decided being a priest was not for me.”

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Undecided about what direction to take, Cruise returned home to his mother and stepfather in New Jersey. Soon after, a knee injury took him off the Glen Ridge High School wrestling team. In its place, he joined the student production of Guys and Dolls, playing the singing-and-dancing role of Nathan Detroit. It changed his life. “I knew what I wanted to be: an actor,” he said. “I felt very comfortable on stage.”

He soon landed a role in the musical Godspell at a local theatre and then headed to Manhattan, skipping his high-school graduation in 1980.

“I went to New York to be an actor.” People who knew him at the time describe Cruise as a long-haired “greaser”, angry, muscular, intense, and obsessed with success. Occasionally he sat in on drama classes at Manhattan’s prestigious Neighborhood Playhouse school. “I couldn’t afford to go all the time because I didn’t have that kind of money.” He did odd jobs – a waiter’s assistant, building superintendent, hauling trash in Harlem. He auditioned for roles. He gave himself a decade to make it as an actor, and succeeded in less than three years.

Nine months after Cruise arrived in New York, he read for the role of David Shawn in the movie Taps. Shawn is the teenage cadet at a military academy who becomes homicidally unhinged during a student rebellion. Taps, a small success in 1981, gave Cruise a career.

“I go to the meeting,” he said, recalling his audition for Taps. “They said, ‘Put up your hair!’ I did. ‘Say this line.’ I said it. They said. ‘Thank you.’ I walked out of the building and started laughing. I thought, ‘I’ll be damned! I didn’t get it.’

I had 25 cents left in my pocket. I was hungry. It was a Friday. I walked down by the Holland Tunnel.” The tunnel takes traffic under the Hudson River from Manhattan to New Jersey. Near its Manhattan entrance, whores once offered oral sex to commuters in their cars.

“There were prostitutes, who used to be around the tunnel, who knew me,” he said. “They’d see me and they’d go, ‘Look, I’ll pick up a john, and you jump in.’ So I’d ride through the tunnel to New Jersey. The driver’s a little like, ‘What’s this guy doing in the back seat?’ But he saw I’m just this 18-year-old kid. I didn’t look dangerous. And they didn’t do anything sexual in front of me. I’d get out in New Jersey and say, ‘Thank you very much.’ Then I’d hitchhike home. That day, when I got home, my mom said, ‘You got Taps!’ A movie! I’ll never forget it. I grew up watching movies,” he continued. “As a kid I’d cut grass and save my money to go to them. When I decided to be an actor, I was thinking of doing theatre and movies. I loved movies and I wanted to make them. It was as simple as that.”

Two years later, Risky Business made Cruise a movie star. He was 21. “When success happened, for me people in the industry changed,” he said. “All of a sudden I was being offered tremendous amounts of money. I went, ‘Uh-oh, be careful.’ You realise that there are people you can’t trust.

I knew from being around my father, who hurt people, that not everyone really means me well. They have similar attributes to him, but they’re actually more clever about it than he ever was.”

It’s a pointed moment of insight into Cruise. The violent father, the uprooted childhood, the school bullies, the dyslexia. A picture emerges of a man still captive to the boy he was, a boy always fretful, braced against the perceived threats; questions and criticism are met with suspicion – someone out to hurt or ridicule him. All that may help explain the combative self-protectiveness, the spin, the act – and the ambition.

Cruise’s success is enormous. The worldwide gross of his more than two dozen films is over $5.6 billion. He has received two Academy Award nominations – the first as best actor for his portrayal of an embittered, paralysed Vietnam war veteran in 1989’s Born on the Fourth of July; the second, a decade later, as best-supporting actor for the misogynistic self-help guru in Magnolia. His new film, Mission: Impossible III, is expected to be a blockbuster.

Cruise’s marital life has not matched the success of his career, something he now recognises. For the first time he speaks about his marriages in something other than the glowing terms he has used in the past. Although he once vigorously declared, “I love women, and I have always trusted women more than men”, and offered by way of example his intense closeness to his mother and three sisters, he did state, early on, that he would never marry. Maybe it was because, as Cruise now admits, adolescent sexuality was no easy passage. “I felt very, very insecure. I was scared to death of being rejected.”

Nevertheless, in 1987, at 24, he married 32-year-old Mimi Rogers, an actress formerly married to a Scientology counsellor, Jim Rogers. She was also a member of Scientology, the quasi-religious cult founded in 1954 by the late Lafayette Ronald (“L Ron”) Hubbard, a writer of sci-fi pulp who flunked out of college and was thrown out of the US Navy. Hubbard famously said: “I’d like to start a religion. That’s where the money is.” Not since the medieval popes has an organised faith charged money for the knowledge of salvation with the rigorous exactitude of the Scientology sect. This has led to lawsuits from disgruntled customers and government fraud investigations. Anyone who joins the group pays a huge sum for each step up the Bridge to Total Freedom, Scientology’s jargon for the pathway to paradise where, at its end, sits the immortal L Ron Hubbard, clear and forever solvent. The trip to join Hubbard and other liberated aliens for trillions of years of bliss can cost hundreds of thousands of pounds. Cruise joined the group in 1990, the dogmatic authority of Hubbard’s sect replacing the father who had abandoned him. Cruise’s union with Rogers, reportedly a mismatch from the start, ended the same year. He blamed its failure on his hectic work schedule. Shortly after, he met the Australian actress Nicole Kidman, then 22, and a Catholic, on the set of Days of Thunder. They married on Christmas Eve 1990. In 1998 they won a libel judgment against the Daily Express for suggesting they were gay and that their marriage was a sham. “It was a lie,” Cruise said.

Homosexuality is a terrible evil to be charged with, according to the canonical writings of Scientology, although being gay may not be as bad as being a psychiatrist. A shrink is about as bad as a human can be, Hubbard wrote, because he is a terrorist who “kills young girls for sexual kicks, murders a dozen patients with an ice pick, castrates a hundred men”. Still, to Hubbard’s way of thinking, homosexuals were almost as dangerous. He decreed that gays “should be taken from society as rapidly as possible… for here is the level of contagion of immorality and the destruction of ethics. No social order will survive that does not remove them from its midst.”

So much for tolerance from Hubbard, a man who never really died, or so his followers believe. Amazingly, Hubbard merely dematerialised like an evaporating spill into a purer dimension of being while hiding out in his trailer, parked near the desert town of Creston, California, in 1986. He was 74, and left promising us to return in the flesh in precisely 13 years. He is still missing.

In addition to loopy philippics against homosexuality, organised religion, psychiatry, journalists and such, Hubbard taught that we are the souls – “thetans” – of exiled aliens captive in human bodies. Xenu, a rogue conqueror in a nasty galactic war 75m years ago, tossed us thetans to planet Earth, casting us into volcanoes, blowing us up with bombs, and insinuating really naughty lies, like the existence of a merciful God, into our little shell-shocked brains. Scientologists, like Cruise, believe all human problems, such as murder, paranoia, sexual dysfunction and depression, stem from these wicked “engrams” (read “ideas”) planted like memories in our “reactive” (read: “subconscious”) minds. And we are condemned to living them over and over again, reincarnated through endless millennia, until we are freed of them, made “clear”, through the ministrations of Scientology. Its confessional lie detectors, a kind of poor man’s psychotherapist, to ferret out these repressed “lies”.

The year after their successful lawsuit against the Express, Cruise and Kidman sued a US supermarket tabloid, The Star, for printing that sex experts were hired to tutor them on physical intimacy for their roles in 1999’s Eyes Wide Shut. The Star retracted the story as untrue. In 2001, two months after celebrating their 10th anniversary, Cruise filed for divorce. Neither party will publicly discuss the reasons for their break-up. Reportedly, they disagreed over religion and the upbringing of their two adopted children. Today Cruise and Kidman share joint custody of Connor, 11, and Isabella, 14. Kidman is now dating the American country singer Keith Urban, who’s about as different from Cruise as you can get.

I asked Cruise about his marriages and if, on balance, they had been happy. “When I think about the marriages I’ve had, I don’t forget the good times I had with those people,” he replies respectfully. But then, for just a fleeting glimpse, the guard drops. “I’m respectful of what we had together. I don’t try to think about every horrible thing there was. But you don’t live life and not know heartache, sorrow and fear. You learn that those things are just part of life. That takes some doing, but it can be done.”

Before I left Cruise, he introduced me to Katie Holmes, who is about 5ft 10in (he is 5ft 7in), brown-eyed, pretty and very pregnant. She wore a large diamond engagement ring. She seemed dazed, passive and vacant. She never stopped smiling. With Holmes in the room, Cruise began trumpeting about how beautiful she was, touching and kissing her like a teenage boy on his first back-seat date, aware he was being watched. I asked if she knew the baby’s gender? She and Tom have their own sonogram machine.“Yes,” she replied, “but we’re not saying.”

Are you happy? I asked her. She nodded yes. Cruise patted her belly. “I am very, very happy!” he exclaimed, grinning his public grin. “I’ve got a baby on the way! My concern is being the best parent I can be, making sure my kids can think and make decisions for themselves. My children are magnificent, and their lives will be their own responsibility.

I know the kind of parent I am and how much I care about my kids.”

He paused. “Let me tell you what happiness is. Happiness is being able to confront life and overcome problems. It’s not running away from life but trying to see life in its full glory.”

The minute Holmes appeared, Cruise’s now-familiar public mode of behaviour had returned. The private man I had seen moments before disappeared into the public persona, the back-slapping camaraderie of a candidate trawling for votes at a party convention. Like a politician, his charm seems overly rehearsed and one wearies of it quickly. His exuberance, coupled with the toothy, practised grin he flashes with disconcerting frequency, is overwhelming in its excessiveness. With it, he dominates those around him, his manner expressing his hunger to be liked, approved and in control.

This bluster, this robust public disguise behind which he hides, struck me as a transparent mask. At heart, I thought, he’s vulnerable, even scared, like the lost boy who never had a close friend.

I found myself liking him because of that.

Mission: Impossible III opens in the UK on May 4