It was a tattoo that almost got Frank Calabrese killed. He'd had it etched across his back while he was in Milan prison in Michigan: a large map of America over which prison bars have been superimposed with a pair of hands reaching out through them in handcuffs. He'd designed it himself, to make a point, he says, about "how you are free in America but somehow not free".

The tattoo was drawn by a fellow inmate, against prison regulations, with the connivance of a guard whom they bribed to look the other way.

Soon after he'd had it done, Calabrese was walking around the prison exercise yard. He was wearing a wire, his torso wrapped in recording equipment like a Christmas tree. Walking beside him was one of the world's most dangerous men – a killing machine from the Chicago mob whose preferred method of assassination was the rope and knife.

Calabrese had just succeeded in enticing the other man into telling him about a succession of murders he'd committed, including that of Tony "The Ant" Spilotro and his brother Michael, immortalised by the film Casino. The unwitting confession was captured by the wire and recorded for later analysis by the FBI.

Suddenly the older man stopped and asked to see Calabrese's new tattoo. "Why've you been covering it up? Let me see it," he said. It was an instant death warrant. If Calabrese lifted up his shirt and revealed the wire, the older man, who was shorter than him but immensely powerful, would know he had been betrayed and would kill him on the spot with his bare hands. It was 300 yards to the prison door and Calabrese calculated he wouldn't make it, deciding instead to stand his ground and bluff it. He pulled his shirt down and refused, saying it would get him into trouble. The older man looked puzzled for a second, then relaxed and backed off.

Frank Calabrese Jr displays his tattoos. Photograph: Fotovitamina for the Guardian

Should Calabrese have been exposed at that moment as an FBI informant, it would have put an end to the largest mafia investigation in American history. As it was, he went on to hold many more hours of taped conversations with the older man that helped to blow apart the Chicago mob. The Outfit, the organised crime syndicate of Al Capone that had terrorised the city for 100 years, had finally got its comeuppance.

That exchange in the prison yard was significant for another, more personal, reason. The older man whom Calabrese was secretly recording, condemning him in the process to spending the rest of his life in prison, had the same name as him: Frank Calabrese. Senior. His father.

Hollywood revealed to Frank Calabrese Jr the truth about his father. Until he saw his own domestic life play out on screen, he'd assumed he was from a normal family.

Home life in the heavily Italian and mafia-frequented neighbourhood of Elmwood Park was dominated by his father's Sicilian roots. Three generations of Italian-Americans – his grandparents, parents and uncles, brothers and cousins – were crammed into the house they called the Compound. Frank Jr was the eldest of three sons, and his father's favourite.

What his father did all day was a mystery to the young boy. When other kids at school asked him how his dad made a living, he was nonplussed.

"Tell them I'm an engineer," Frank Sr would say.

"What, like a choo-choo-train engineer?"

"No, tell them I'm an operating engineer."

Calabrese was 12 when The Godfather came out. The Corleone family it portrayed was strikingly similar to his own. Art was imitating life, or was it the other way round? His father was friendly with Gianni Russo, who played Carlo Rizzi, the Godfather's son-in-law, in the movie. One night, Russo was being interviewed on a show and pulled out a knife he said had been given to him by a mobster.

"I gave him that knife," Frank Sr said as they sat watching TV.

Years later, in one of the taped conversations Frank Jr had with his father, Calabrese Sr remarked that Mario Puzo's account in the original book of the initiation ceremony for "made men" was spot on. "Whoever wrote that book, either their father or their grandfather or somebody was in the organisation," said Calabrese Sr, who, as a "made man" himself, knew what he was talking about.

"So you mean they actually pricked the hand and the candles and all that stuff?" Frank Jr asked.

Frank Calabrese Sr. Photograph: AP

"Their fingers got cut and everybody puts the fingers together and all the blood running down. Then they take pictures, put them in your hand, burn them. Holy pictures."

A few years after The Godfather came out, Frank Sr began to draw his son into the family business. It was a slow, almost imperceptible process. "He started to involve me in little things," Calabrese said. "It was like, 'Hey, son, do this for your dad. Go take this envelope, go deliver this to a store.'"

Calabrese was encouraged to keep a low profile. "We were taught to blend, to fly under the radar. My father told me to drive Fords and Chevies, not Cadillacs or BMWs. Wear baseball caps, not fedoras, ski jackets, not trenchcoats."

At 19, Calabrese was allowed to take part in mob activities, starting with collecting money from peep shows and graduating into keeping the books. It was an education of sorts. "I learned all my maths through the juice loan business." As he became more central to his father's racketeering and gambling concerns, the lessons became more specific. Calabrese was shown by his father how to hug someone to see if they were carrying a gun or wearing a wire.

Calabrese embraced his new life. "When I bought into it, I bought into it strong. Whatever my father told me to do, that's what I did. I didn't fear law enforcement, or jail, or death. If my father told me to walk full-speed into that wall, I would."

Then, at the age of 26, Calabrese was invited to take part in an initiation ceremony all of its own – his first gangland murder.

For a key prosecution witness in a massive mob case that took down 14 top mafia bosses, Frank Calabrese Jr comes across as remarkably relaxed. He's not in a witness protection scheme, lives under his own name, and when I visit him in a condo apartment outside Phoenix in Arizona, he readily opens the door and welcomes me in without so much as a frisking. How does he know I'm not a hit man sent from Chicago to exact revenge?

"I don't," he says.

Calabrese looks the part of a Chicago hard man. His head is shaved, accentuating his large ears and piercing blue eyes. He's wearing a sleeveless vest and slacks, which display the product of hours spent pumping iron. When he speaks, though, Calabrese does so with a surprising softness and introspection. It's a bit like listening to Tony Soprano talking to his therapist (Calabrese is a big Sopranos fan – he watched the whole series with his mother and ex-wife, wincing at the parallels with his own family).

Hanging on the wall of his apartment is a framed photograph of Frank Sinatra, Dean Martin, Peter Lawford and Sammy Davis Jr from the original Ocean's 11. His father, he explains, was friendly with Sinatra's bodyguard.

It was feared underboss Angelo 'The Hook' LaPietra who 'whistled in' Frank Sr to the Outfit.

Frank Calabrese Sr – aka Frankie Breeze – was born in 1937 into a poor Italian family on the west side of Chicago. He left school at 13 and could barely read and write. By 16 he had begun to make money as a thief and later developed a "juice" loan business, extracting exorbitant rates of return. It was a lucrative enterprise: at its peak he had $1m out on loan with collections of up to 10% per week. After the trial ended and the elder Calabrese was given multiple life sentences, the FBI searched his home and found $2m-worth of diamonds and almost $800,000 in bills and property deeds.

In 1964, Calabrese Sr was "whistled in" to the Outfit by a much-feared mafia underboss called Angelo "The Hook" LaPietra. The nickname came from what LaPietra would do to anyone who fell behind with their loan repayments: hang them on a meat hook and torture them with a cattle prod or blowtorch. Cause of death – suffocation from screaming. The younger Calabrese grew up thinking of LaPietra as "Uncle Ang".

Together with LaPietra and his own brother, Nick, Calabrese Sr developed a specialist role as the Outfit's murder squad. Calabrese Jr was given an insight into that as a teenager one night when his father came home and hurried him into the bathroom. With the fan on and the water running so no one else could hear, he breathlessly recounted a hit he'd just carried out. "We got 'im… Our guy wasn't listening to the rules, so we shotgunned him."

Those who were "retired" by Calabrese Sr and his brother included Michael "Bones" Albergo; John Mendell, who rather foolishly robbed the home of the Outfit's consigliere, Tony "Big Tuna" Accardo; a business rival called Michael Cagnoni, who was blown up in his car; rogue mobster Richard Ortiz; and Emil Vaci, a Las Vegas-based gangster the Outfit feared might inform against them. Then there were the Spilotros of Casino fame. Tony Spilotro was head of the Outfit's Vegas arm, running a gambling and "skimming" business (skimming off casino profits without telling the tax authorities). He got too big for his boots, and when the bosses found out he was having an affair with another made man's wife, they wanted him gone.

Tony Spilotro and his brother Michael were lured to Chicago under the pretext that Michael would be "made" and Tony would be promoted to capo. Instead, they had ropes thrown around their necks and were strangled – the legendary "Calabrese necktie".

The younger Calabrese's own brush with murder came in 1986 when he was chosen to take part in a hit on John "Big Stoop" Fecarotta. He was to sit in the back seat of the getaway car. "I was ready to murder for my dad," Calabrese says. "You always need two guys in the car, and I was to go with my uncle Nick. If I'd crossed that line, there would have been no coming back. But my uncle talks me out of it. He tells me, 'This ain't for you. You don't want this life.' He saved me."

That was a turning point for Calabrese, in both his relationship with the mob and, by extension, with his father. When he was young, his father was loving towards him, always ready with a hug. But as Calabrese Sr came increasingly under the influence of the murderous LaPietra, he changed, growing colder and more brutal towards his son.

"His temper became shorter, he would be quicker with his hands, more controlling. He didn't think twice about cracking you in the face."

The younger Calabrese came to see how manipulative his father was, switching personalities at the click of his fingers. "If you were sitting with him here right now, you'd love him. He'd charm you. But when you'd gone, he'd turn into his second personality – a controlling and abusive father. And his third personality was the killer."

To try to wriggle out of his father's tight embrace, Calabrese set up in business on his own. He opened Italian restaurants, and later began dealing cocaine. He kept that hidden from his father, knowing that if he was found out "the old man would have killed me". He also kept secret his own intensifying addiction to the drug. In a desperate move to break free and to keep his habit fed, Calabrese began stealing from a cache of about $700,000 in $50 notes his father had tucked behind a wall in his grandmother's basement.

Not a good idea. When his father discovered the losses, and who was responsible, he issued a decree. "From now on, I own you," he told his son. "The restaurants are mine, your house is mine, everything is mine."

A few months later his father asked Calabrese to join him for a coffee. They met at a lock-up garage used by the crew. "As I opened the door I realised, oh shit! He's setting me up. He slams the door, turns and sticks a gun in my cheek. Then he says: 'I would rather have you dead than disobey me.'"

Calabrese started sobbing and begging for forgiveness. "Somehow I got out of that garage. As we got back in the truck, he started punching me and back-handing me in the face. My tears were rolling down and all I could think about was how I could never trust this man again. From that day on, I have never trusted anybody. Nobody."

The decision to turn informant against his own father was taken in 1998 inside Milan prison where both Frank Calabreses were sent after being found guilty of racketeering and illegal gambling. Imprisonment was the best thing that happened to the younger man. It allowed him to kick his cocaine addiction, and to become healthy once again. Most important, it freed him from his father's control.

He became determined that as soon as he was released he would make a new life for himself. "I decided that I was going to quit the Outfit. I'd wound up in prison, on drugs. That wasn't what I wanted any more. I had to find a way to go straight when I came out."

But he knew a huge hurdle stood in his way: his father. He had a choice. Either he could wait until they were both out, then confront his father and tell him he wanted to leave the family business, in which case there would almost certainly be a showdown and one of them would end up dead.

Or he could cooperate.

The FBI called their investigation Operation Family Secrets. The 2007 trial lasted three months and took into account 18 murders. In addition to his father's life sentences, long prison sentences were eventually handed out to seven other Outfit bosses. It was an extraordinary result given the history of the Chicago mob. In its 100 years, the Outfit had committed more than 3,000 murders, yet before this only 12 convictions had been secured. Until Calabrese took the stand, backed up by his uncle Nick, who had also turned prosecution witness, not a single made member had been held accountable.

During the trial, the younger Calabrese gave evidence against his father standing just feet away from him in the courtroom. "The one thing I wasn't ready for was the emotional part. I walk into the courtroom and it's the strangest feeling I've ever had. There was my dad. Part of me wanted to go over to him and hug him and say, Dad, I'm going to take care of you. It's going to be OK. Man, I wasn't prepared for that."

As he left the courtroom at the end of his testimony, "the tears just started streaming. An agent asks me, 'Are you OK?' And I say, 'No, I've just realised that's the last time I'll ever see my dad.'"

He was right about that. The elder Calabrese, now 74, is being held in a maximum security institution in Missouri where he has been kept for the past two years in almost total isolation. He is permitted no visitors, nor any contact with other prisoners in a regime reserved for a handful of the most serious terrorists and serial killers.

Calabrese left Chicago after the trial and moved to Phoenix, partly to get away from his past and partly because the hot, dry air of Arizona is good for his health. A few years ago he discovered he had MS and though he keeps it at bay with exercise, it causes him to limp.

He lives with his two children, Kelly and Anthony, and makes a living as a motivational speaker, telling law-enforcement conferences and self-help groups how he has turned his life around. He is unmarried, but his former wife Lisa lives nearby and they remain close. She is still deeply afraid, he says, that his father will seek retribution and she has pleaded with him to enter witness protection. But he continues to refuse. As he writes in his book: "I'm pragmatic. If people can kill presidents, they can kill me. Nobody is invincible and completely safe in today's world."

When I ask to see the tattoo that nearly got him killed, he pulls up his shirt to reveal that his back carries not only the drawing of the map of America with prison bars, but also seven small tattoos depicting bullet holes – like the ones you get on cowboy posters.

"I feel I'm always going to have to watch my back," he explains, "so those bullet holes are a reminder to me to be alert every day."

Regrets, he has a few. He still finds it difficult to come to terms with the fact that he committed the mobster's ultimate sin by ratting on another. And though he is convinced he made the right decision, he is still deeply troubled by the outcome. "At this stage in his life, as my dad gets old, I wanted to be there for him. I wanted to be his protector, not his executioner."

Can there be forgiveness between them, the Frank Calabreses?

"I can forgive him. I love my dad to this day, I just don't love his ways. But I don't think he can forgive me. I really don't. I wish he could."

Calabrese says he's resigned to the grip his father has, and will for ever have, over him. "I know in my heart that the day my father dies he'll haunt me," he says. "This will go on for eternity. I don't know what to expect in the next life, but I do know that wherever it is he will be waiting there for me. And he's not going to be happy with me."

• Operation Family Secrets: How A Mobster's Son And The FBI Brought Down Chicago's Murderous Crime Family, by Frank Calabrese Jr, is published in the US by Broadway Books.