At 78, Robert Pirsig, probably the most widely read philosopher alive, can look back on many ideas of himself. There is the nine-year-old-boy with the off-the-scale IQ of 170, trying to work out how to connect with his classmates in Minnesota. There is the young GI in Korea picking up a curiosity for Buddhism while helping the locals with their English. There is the radical, manic teacher in Montana making his freshmen sweat over a definition of 'quality'. There is the homicidal husband sectioned into a course of electric-shock treatment designed to remove all traces of his past. There is the broken-down father trying to bond with his son on a road trip. There is the best-selling author of Zen and the Art of Motorcycle Maintenance, offering solutions to the anxieties of a generation. And there is, for a good many years, the reclusive yachtsman, trying to steer a course away from cultish fame.

Pirsig doesn't do interviews, as a rule; he claims this one will be his last. He got spooked early on. 'In the first week after I wrote Zen I gave maybe 35,' he says, in his low, quick-fire Midwestern voice, from behind his sailor's beard. 'I found it very unsettling. I was walking by the post office near home and I thought I could hear voices, including my own. I had a history of mental illness, and I thought: it's happening again. Then I realised it was the radio broadcast of an interview I'd done. At that point I took a camper van up into the mountains and started to write Lila, my second book.'

It is that second book, recently republished, that has prompted him to talk to me now. He sits in a hotel room in Boston and tries, not for the first time, to make some sense of his life. He is, he suggests, always in a double bind. 'It is not good to talk about Zen because Zen is nothingness ... If you talk about it you are always lying, and if you don't talk about it no one knows it is there.' Generally, rather than analysing, he says, he would rather 'just enjoy watching the wind blow through the trees'. Reclusion has its discontents, however. 'In this country someone who sits around and does that is at the bottom of the ladder, but in Japan, say, someone who goes up into the mountains is accorded great respect.' He pauses, laughs. 'I guess I fall somewhere in between.'

Ever since I first read Pirsig's motorbike quest for meaning, when I was about 14, I've been curious to imagine its author. Part of the compulsion of that book, which has sold more than five million copies, is the sense of autobiographical mysteries that remain unexplained. While Pirsig's narrator tries to marry the spirit of the Buddha with western consumerism, discovers the godhead in his toolkit, and intuits a sense of purposive quality independent of subjects and objects, he also constructs a fragmentary picture of his own past. His pre-shock-treatment former self, the ghostly Phaedrus, haunts his travels across the Midwest.

'What I am,' he writes at one point, 'is a heretic who's recanted and thereby in everyone's eyes saved his soul. Everyone's eyes but one, who knows deep down inside that all he has saved is his skin.' My 14-year-old self double-underlined this and put two Biro exclamation marks in the margin. Twenty-six years, and several revisionist readings of the book later, I'm still wondering what Pirsig thinks of when he thinks of himself.

He suggests a lot of that idea still goes back to his childhood as a disaffected prodigy. He says that ever since he could think he had an overwhelming desire to have a theory that explained everything. As a young man - he was at university at 15 studying chemistry - he thought the answer might lie in science, but he quickly lost that faith. 'Science could not teach me how to understand girls sitting in my class, even.'

He went to search elsewhere. After the army he majored in philosophy and persuaded his tutor to help him get a place on a course in Indian mysticism at Benares, where he found more questions than answers. He wound up back home, married, drifting between Mexico and the States, writing technical manuals and ads for the mortuary cosmetics industry. It was when he picked up philosophy again in Montana, and started teaching, that Phaedrus and his desire for truth overtook Pirsig once more.

At that time, he recalls, in his early thirties, he was so full of anxiety that he would often be physically sick before each class he taught. He used his students to help him discover some of the ideas that make up what he calls the 'metaphysics of quality' in his books, the ideas that led him to believe that he had bridged the chasm between Eastern and Western thought. No two classes were the same. He made his students crazy by refusing to grade them, then he had them grade each other. He suggests that by the end of each term they were so euphoric that if he had told them to jump out of the window they would have done. The president of the university gave a speech, and he contradicted him in the middle of it by shouting: 'This school has no quality.' He saw clearly how American society was disconnected from life and he believed he could help it connect. He was reading Kerouac, and trying to live in truth.

Alongside that, I say, as he describes that time with some fervour, I guess there was some depression setting in? 'Well,' he says, 'there was fear. All these ideas were coming in to me too fast. There are crackpots with crazy ideas all over the world, and what evidence was I giving that I was not one of them?'

Such evidence proved harder and harder to present. One day in the car with his six-year-old son Chris, his mind buzzing, Pirsig stopped at a junction and literally did not know which way to turn. He had to ask his son to guide him home. What followed was the point where he either found enlightenment, or went insane, depending on how you look at it (really the root of all the questions in his first book).

'I could not sleep and I could not stay awake,' he recalls. 'I just sat there cross-legged in the room for three days. All sorts of volitions started to go away. My wife started getting upset at me sitting there, got a little insulting. Pain disappeared, cigarettes burned down in my fingers ...'

It was like a monastic experience?

'Yes, but then a kind of chaos set in. Suddenly I realised that the person who had come this far was about to expire. I was terrified, and curious as to what was coming. I felt so sorry for this guy I was leaving behind. It was a separation. This is described in the psychiatric canon as catatonic schizophrenia. It is cited in the Zen Buddhist canon as hard enlightenment. I have never insisted on either - in fact I switch back and forth depending on who I am talking to.'

Midwestern American society of 1960 took the psychiatrist's view. Pirsig was treated at a mental institution, the first of many visits. Looking back, he suggests he was just a man outside his time. 'It was a contest, I believe, between these ideas I had and what I see as the cultural immune system. When somebody goes outside the cultural norms, the culture has to protect itself.'

That immune system left him with no job and no future in philosophy; his wife was mad at him, they had two small kids, he was 34 and in tears all day. Did he think of it at the time as a Zen experience?

'Not really. Though the meditation I have done since takes you to a similar place. If you stare at a wall from four in the morning till nine at night and you do that for a week, you are getting pretty close to nothingness. And you get a lot of opportunities for staring in an asylum.'

When he was released, it only got worse. He was crazier; he pointed a gun at someone, he won't say who. He was committed by a court and underwent comprehensive shock treatment of the kind described by Ken Kesey in One Flew Over the Cuckoo's Nest

I wonder if he remembers the mechanics of it?

'Well they put a little rubber thing in your mouth and then they gave a drug like curare, used by South American Indians in their darts. It stops your lungs before it stops your mind. Before you go under you had a feeling like you were drowning. I woke up one time and I thought: where the hell am I? I had a feeling I was in my Aunt Flossie's house, which I had liked as a child. I thought I must have passed out drunk.' He laughs. 'This was after the 14th treatment I think.'

When his wife came to see him he knew something was wrong but he did not know what it was. A nurse started to cry because she knew that his wife had divorced him while he had been in hospital. 'The funny thing about insane people,' he says, 'is that it is kind of the opposite of being a celebrity. Nobody envies you.'

Pirsig was able to keep a tenuous grip on his former self, despite the treatment. He figured that if he told anyone he was in fact an enlightened Zen disciple, they would lock him up for 50 years. So he worked out a new strategy of getting his ideas across. He embarked on a book based on a motorcycle ride he made with his son, Chris, from Minnesota to the Dakotas in 1968. 'It was a compulsive thing. It started out of a little essay. I wanted to write about motorcycling because I was having such fun doing it, and it grew organically from there.'

When the book came out, in 1974, edited down from 800,000 words, and having been turned down by 121 publishers, it seemed immediately to catch the need of the time. George Steiner in the New Yorker likened it to Moby Dick. Robert Redford tried to buy the film rights (Pirsig refused). It has since taken on a life of its own, and though parts feel dated, its quest for meaning still seems urgent. For Pirsig, however, it has become a tragic book in some ways. At the heart of it was his relationship with his son, Chris, then 12, who himself, unsettled by his father's mania, seemed close to a breakdown. In 1979, aged 22, Chris was stabbed and killed by a mugger as he came out of the Zen Centre in San Francisco. Subsequent copies of the book have carried a moving afterword by Pirsig. 'I think about him, have dreams about him, miss him still,' he says now. 'He wasn't a perfect kid, he did a lot of things wrong, but he was my son ...'

I ask what Chris thought of the book, and Pirsig's face strains a little.

'He didn't like it. He said, "Dad, I had a good time on that trip. It was all false." It threw him terribly. There is stuff I can't talk about still. Katagiri Roshi, who helped me set up the Zen Centre in Minnesota, took him in hand in San Francisco. When Katagiri gave Chris's funeral address tears were just running down his face. He suffered almost more than I did.'

When his son died, Pirsig was in England. He had sailed across the Atlantic with his second wife, Wendy Kimball, 22 years his junior, whom he had met when she had come to interview him on his boat. She has never disembarked. He was working at the time on Lila, the sequel to his first book, which further examines Phaedrus's ideas in the context of a voyage along the Hudson, with Lila, a raddled Siren, as crew.

The book is bleaker, messier than Zen and the Art of Motorcycle Maintenance, though it carries a lot of the charge of Pirsig's restless mind. 'If I wrote it today,' he says, 'it would be a much more cheerful book. But I was resolving things in Lila; the sadness of the past, and particularly Chris's death, is there. Zen was quite an inspiring book, I think, but I wanted to go in the other direction with Lila and do something that explored a more sordid, depressing life ...'

He hoped Lila would force the 'metaphysics of quality' from the New Age shelves to the philosophy ones, but that has not happened. Though a website dedicated to his ideas boasts 50,000 posts, and there have been outposts of academic interest, he is disappointed that his books have not had more mainstream attention. 'Most academic philosophers ignore it, or badmouth it quietly, and I wondered why that was. I suspect it may have something to do with my insistence that "quality" can not be defined,' he says.

This desire to be incorporated in a philosophy canon seems odd anyhow, since the power of Pirsig's books lie in their dynamic personal quest for value, rather than any fixed statement of it. But maybe eventually every iconoclast wants to be accepted.

He still sails. He lives in rural New England and has just been up to the islands of Maine with his wife on the same boat that he describes in Lila - perfectly maintained, of course. He lives these days in cyberspace, he says, where his ideas circulate. He plans to learn to tango, and visit Buenos Aires. He's just discovered YouTube. He doesn't write any more, though, and he hardly reads. I wonder if that old depression ever returns?

'I've been hit with it lately,' he says. 'It did not seem related to my life in any way. I have money, fame, a happy wife, our daughter Nell. But I did for the first time go to a psychiatrist. He said it's a chemical imbalance and he prescribed some pills and the depression has gone.'

Otherwise, he says, he tries to live as best he can to the dictates of 'his dharma': to stay centred. I ask if he fears death.

'I'm not depressed about it,' he says. 'If you read the 101 Zen Stories you will see that is characteristic. I really don't mind dying because I figure I haven't wasted this life. Up until my first book was published I had all this potential, people would say, and I screwed up. After it, I could say: No, I didn't screw up.'

He smiles. 'It was just that I was listening to a different drummer all along.'

Pirsig's pearls

· The Buddha resides as comfortably in the circuits of a digital computer or the gears of a cycle transmission as he does at the top of a mountain.

· Metaphysics is a restaurant where they give you a 30,000 page menu and no food.

· Traditional scientific method has always been, at the very best, 20-20 hindsight. It's good for seeing where you've been. It's good for testing the truth of what you think you know, but it can't tell you where you ought to go.

· Why, for example, should a group of simple, stable compounds of carbon, hydrogen, oxygen and nitrogen struggle for billions of years to organise themselves into a professor of chemistry? What's the motive?

· The only Zen you find on the tops of mountains is the Zen you bring up there.

Now and Zen

Born 6 September 1928, Minneapolis.

Family Father was a law lecturer and mother was Swedish-born. Pirsig married Nancy Ann James in 1954. They had two sons: Chris, and Ted, now 48. Now married to journalist Wendy Kimball, with whom he has a 25-year-old daughter, Nell.

Education Judged to have an IQ of 170 at age nine. Went to University of Minneapolis at 15, but joined the army in 1946, serving in Korea before returning to the university to study philosophy. Then studied at Benares in India.

Zen and the Art of Motorcycle Maintenance Appears in Guinness Book of Records as the bestselling book rejected by the largest number of publishers (121). Sold 5m copies worldwide.

· Lila is published by Alma Books (£7.99). A slipcased, signed limited edition is available at selected Waterstone's (£45)