Anita Thompson tosses back her blonde hair, pours herself another cup of tea and rolls her eyes. “I’m going to get hell for this interview,” she says. Since her husband Hunter S Thompson, the king of gonzo journalism, shot himself with a .45calibre pistol in February 2005, her life has been tricky. According to her, his family no longer speak to her and important factual details about her husband’s death are only now emerging.

Anita and Thompson had been married for just two years when he killed himself. They were an unlikely pairing: 35 years his junior, Anita was a snowboarding nanny from Colorado when she met the scourge of American polite society. She had confessed to a friend that she did not know much about American football. “My friend said, ‘I have the perfect person to introduce you to the game. He is a sports writer and his name is Hunter S Thompson’.”

She had vaguely heard of him but had never read his work. Not his chronicle of living with the Hell’s Angels or any of his various pieces of journalism; not even his masterpiece, Fear and Loathing in Las Vegas – that seminal 1972 novel in which Thompson, thinly disguised as crazy hack Raoul Duke, goes with his Cuban attorney on a drug-and-booze-fuelled jaunt to the gambling capital of Nevada.

Perhaps her ignorance was just as well. Through his writing, Thompson comes across as an alarming figure, capable of living above all known limits of excess. In the event, she says, “we became instant friends. I fell in love with his voice on the phone even before meeting him”. Although eloquently aggressive on the page, Thompson was apparently every inch the gent: “He was a gracious and a beautiful man. I was very comfortable with him.”

He hired her as his “researcher, editor, photocopier and cook” and she moved into his sprawling home – Owl Farm in Aspen, Colorado – a year later in 2000. Although he continued to be gentlemanly in his ways, it was clearly a feisty relationship.

“We were always fighting,” Anita admits. “We started fighting almost the day we met, but the fights were pretty dramatic towards the end.” She pauses. “We had pretty loud fights. We were pretty intense people.

“We had to make a living, so my job was to get him to write, and his job was to write so we could pay the bills. So there was tension there. We were always on deadline.”

That must have been rather tricky, what with all the booze and drug-taking, both synonymous with the Thompson lifestyle. Anita has admitted that she had a serious drug problem for a while – but she knocked that, and her boozing, on the head after her entry into the wired, weird world of friends and hangers-on that was Owl Farm.

“I remember looking around one day and I thought, I can’t keep up with this lifestyle and these people – I have to sober up,” she says.

In 2003 she and Thompson got married. Rather a bourgeois move for a dyed-in-the-wool hell-raiser, one would think – but Thompson, then 65, was no idiot. He had just witnessed the chaotic goings-on after a close friend had died intestate. Without the benefit of a will or a marriage certificate, the friend’s bereaved girlfriend had been left high and dry while the family had grabbed everything. Thompson did not want this to happen to Anita.

“Hunter was having back surgery,” she explains, “and he said, ‘If anything happens to me during the operation, they [his former wife and son] will eat you alive’. So we had a civil ceremony, very small and private. Just for that piece of paper.”

At the time Anita thought it was all rather unnecessary: “The way it’s been put to me since is that every second wife will always be attacked by the children of the first wife. And not to take it personally.” And that is precisely what she says happened.

On the day of Thompson’s death, the scene unfolded thus: his only son, Juan, from his former marriage, was down from his home in Denver and staying at Owl Farm with his wife and son Will, 7. The night before, Thompson – who loved to perform pranks and adored anything to do with guns, had decided to combine both passions.

“He was pointing a pellet gun around the house and aimed it at a gong next to my head,” says Anita. Although the image of Thompson capering around with an air rifle could have come straight from the Fear and Loathing archive, Anita was not amused: “I had never seen him act that crazy around the house. He was very careful and responsible with guns. This was the first time I had seen him be so sloppy – particularly with Will in the room.”

His behaviour provoked a huge row. “We had been in a fight over that, and the next day I was still angry about the night before,” she says. It was at that point that she went off to her yoga class at the gym, 26 minutes away by car.

When she arrived at the parking lot, she called Thompson. “We had a private, sweet conversation. Thank God. We had a really beautiful talk on the phone. He said, ‘Come home, everything’s fine, don’t worry, I love you more than ever. Come home and we’ll write a column tonight’. I thought it was his way of making up. Because if we wrote together, the fighting would stop.”

Anita’s brown eyes are full of tears. “While he was writing,” she goes on, “he would like to have a beautiful dinner, me nicely dressed, flowers. He liked beauty around him. It helped him work.”

After their reconciliatory chat, something odd happened. “He didn’t hang up. He put the phone on the counter. I heard some clicking. And I thought he was tapping on his typewriter. What he was doing, of course, was cocking his gun.”

Their conversation had lasted from 5.16pm to 5.26pm. The official time of death was 5.42pm: “So he did it almost straight away.”

Not that she had any inkling of his intention. She did her yoga and then had a shower. “I had all this conditioner on my hair,” says Anita, now openly weeping. “And a friend came over and said, ‘Is Hunter okay?’ And I said, ‘Yes, judging from our last conversation’. But she was pale, her lips were white. And she said, ‘I’ll stay with you while you check your messages’. And there was a message from Juan. He said, ‘Come home, Anita. He’s dead’.”

Thompson had put one of his favourite guns in his mouth and shot himself through the head while sitting in his chair in the kitchen. That night, in a scene worthy of a David Lynch film, close friends apparently came over to pay homage to the great writer while his corpse was still in the chair. Chivas Regal (his favourite drink) was flowing and a blank piece of paper was put in his typewriter.

Does Anita think he was drunk when he shot himself? She shakes her head. “Hunter was never drunk. He would be drinking from the moment he woke up to the moment he went to sleep, but you would never see him drunk. He had a remarkable constitution, which was why so many people couldn’t last in the kitchen with him because they would try to keep up and they couldn’t.”

That night Anita cut off her foot-long ponytail, which she placed on his body prior to its cremation. The ashes of Hunter S Thompson were eventually fired over Owl Farm in a rocket during a memorial service attended by guests including Sean Penn, Bill Murray and Johnny Depp (star of the movie version of Fear and Loathing).

If that all sounds perfect, it was anything but. Anita claims that Hunter’s family turned on her almost before his body was cold.

Three days after the death, Juan issued a press release announcing that the family had been expecting his father to kill himself. “I was like: what do you mean we expected this?” says Anita. “And Jennifer, Juan’s wife, said, ‘Yeah, we knew he would do this within six months’.”

Then Juan announced to the press that he was going to take over the Thompson literary reins from his father. Anita recalls Juan saying: “My dad told me, ‘Don’t kid yourself, son, I passed on the gift’.” She is most tactful about whether or not Juan did indeed inherit Thompson’s considerable gifts. But she does add: “At the time, Juan was working as a computer technician at Chipotle, a Mexican chain restaurant.” Ah.

There was also the thorny question of Thompson’s “legacy”. Juan was burning to handle the Thompson myth in a bookish, reverent manner, which would no doubt have pleased the legions of undergraduates who now take Hunter S Thompson courses. But this idea did not find favour with Anita.

“Juan believes Hunter’s legacy is for the scholars. But Hunter loved his readers. When he died, I got boxloads of letters – hundreds and hundreds – and at the memorial I wanted there to be a place for Hunter’s fans. Juan said, ‘No, we’ll invite the fans to the next memorial’. But then again, six months later, his readers were excluded.”

Anita now wants to turn Owl Farm into a writers’ residence and a place where adults and children can come to learn about Thompson. She has kept it just as he left it – even down to the bizarre knickknacks: old pairs of spectacles, stuffed animals and the handwritten notes that plaster the kitchen walls (“Let’s get stoned and have orgasms and laugh a lot” is a typical example). Juan, however, wants the items left to him and the family in the will removed from the house and distributed. “Technically, he has the right to do this, but I want to keep it frozen in time,” says Anita.

She claims that, in happier times, “Juan and I were very close”. Not now. These days, she says, the Owl Farm trustees act as a bulwark between them.

Three years on from Hunter’s death, Anita is obviously still distraught and emotionally vulnerable. She has come to Europe for a respite from what must be a lonely life in the ramshackle building that is still saturated with reminders of her husband.

But she is definitely going back: “I feel safe at Owl Farm. It’s thanks to Hunter and his wishes that I am there.”

Thompson’s will makes it clear that the farm and its 45 acres of beautiful Colorado land are Anita’s rightful home until her death. It is probably the largest single asset that he left behind (she claims that he did not die a wealthy man).

Does she wonder whether his family suspect her of influencing what Thompson wrote in his will? “People didn’t think I had a hand in it,” she says.

She then goes on to recount a bizarre tale involving a piece of paper which Juan said that Hunter had dictated to him as he was dying. It appeared to be a codicil to the will – but it was eventually held to be invalid.

So what did it say? “Oh, something about one trustee . . . and some other issues.”

Crucially, she says, there was no investigation directly after the death. “Maybe the sheriff didn’t want to upset Juan by asking too many questions,” Anita speculates. But there were some anomalies.

“The gun that Hunter shot himself with was a semi-automatic. Normally, when you shoot a weapon like this, the next bullet goes into the chamber; but in this case there was no bullet in the chamber.” She shrugs. “I don’t think about this all the time.”

Where was Juan when Thompson shot himself? “In the other room. He said it sounded like a book dropping.” She obviously has questions that she wants to ask him about the evening his father died. But, she says, “Juan and I don’t speak any more so I can’t get answers from him.”

Recently, the local coroner sent her photographs of the scene of death which she claims have fundamentally changed her understanding of that evening. She refuses to be drawn on what they show, but insists that they are crucial, demonstrating that something she was told at the time was incorrect.

However, she has no doubt that Thompson committed suicide. In the note he left for her, she says, “he wrote that it wasn’t fun any more, that he wasn’t fun any more. And that he had lived 50 years longer than he needed or deserved to. It wasn’t so much an apology as an explanation”.

Does she feel she failed him? “Oh, I did. The job of a wife is to protect your husband when there are dark forces around, or when he is feeling dark and depressed. I failed at it.”

The biggest problem was his health; after an operation on his back, Thompson fell over and broke a leg while on a faintly improbable assignment to cover the Honolulu marathon. This reignited the back problems and raised the spectre of yet another operation – which he dreaded.

“But he had so much more work ahead of him. He was so much fun,” says Anita. Still in thrall to him, despite all the arguments, she has just written a book called The Gonzo Way – a thoroughly readable account of Thompson’s philosophy and final years.

“The best thing about our marriage was that it was like being married to a teenage girl trapped in the body of an elderly dope fiend,” says Anita. “Which was also the hardest thing about our marriage.”

She sighs and wells up again: “As of January 1 this year, I thought I’d start dating again. But I miss him. I’ve realised it’s going to be a challenge finding anything interesting in life after his death. But the last thing he would want me to do is to spend the rest of my days simply mourning.”

She’s right. It’s not the Gonzo Way.

The Gonzo Way: A Celebration of Dr Hunter S Thompson, by Anita Thompson, is published by Fulcrum Publishing