Interview: Philip Pullman - Author

"I've had letters about my wickedness for many years now," he says, wearily. "I don't take them very seriously. I'm not angry with these people. They think they're doing me a favour by warning me about the awful consequences of what I'm doing. I'm sure if I could sit down and spend half an hour with them, make them a cup of coffee or something, we'd all get on very well."

What really matters, you see, says Pullman, is not what you believe but how you behave. Therefore, however wearied he might be at the sight of another journalist on his doorstep, the third today and not the last, he makes me a cup of tea. He is courteous but distant, as if a certain formality lingers from his days as a teacher.

To describe the trilogy – Northern Lights, The Subtle Knife and The Amber Spyglass – as I did above is misleading. More than any of their offbeat theology, they are rollicking adventures, teeming with epic quests, resourceful heroes, infinite worlds and creatures, from armoured bears to spies six inches high.

His inventiveness as a fantasy writer tends to be overshadowed by his role as one of Britain's better-known atheists. Then again, having dared to write a provocatively titled book about Jesus for Canongate's myths series, what can he expect?

If it's controversy you're looking for, The Good Man Jesus and the Scoundrel Christ doesn't disappoint. Pullman's Virgin Mary (she isn't, of course) has twin sons, Jesus and Christ. Jesus, a mischievous child, grows into a thoughtful, passionate man who leaves carpentry to preach love, transformation and the Kingdom of God. His twin skulks in his shadow, half admiring, half envious, chronicling a slightly altered version of events for posterity at the behest of a mysterious "stranger".

While great swathes of the book draw directly on the Gospels, Pullman argues that events have been distorted by the church, in particular by the Apostle Paul, who emphasises "Christ" over "Jesus". There are no miracles – the sick are "uplifted by (Jesus's) presence", not healed – and the convenient device of an identical twin takes care of the "Resurrection". Pullman's Jesus is a good man caught up in events he barely understands, who dies in vain for a God in whom he realises he no longer believes.

For anyone who hasn't stopped reading at this point (and there will be some) there is more. Both Jesus and Christ are surprisingly nuanced characters. Pullman clearly has affection for both of them. Jesus is strong, charismatic, principled. Christ is smart, doubt-ridden, self-aware; in essence, more modern.

"The one who surprised me was Christ," says Pullman. "I was pleased to find, but hadn't really expected, that Christ was developing as a character as I wrote him. He acquired a depth and complexity and self-awareness which was surprising to me. But that's how fictional characters behave. And one of the things I hope readers will take away from this book is that, whereas Jesus probably did exist, Christ was a fiction."

What is more interesting still is why, as someone who has long departed the Christian faith, he wanted to write it at all. He is an intuitive writer who speaks about being drawn to a story which has "a shape that you want to caress". As a non-believer, he is still drawn to the shapes and forms of the faith he no longer has.

He is almost belligerent. "This is a story that belongs to me. I was brought up in the Christian religion, this story is part of what made me. It's intricately and intimately bound up with everything I've done since, everything I've thought and felt. I have a right to tell it, and if it offends someone, well, that's bad luck."

Pullman came into Christianity under the influence of his maternal grandfather, an Anglican clergyman. In his church, he learned the hymns, heard the stories.

"He used to delight in spotting references to the Bible. He enjoyed the old Tate & Lyle Golden Syrup tin. 'See that, my boy? Out of the strong came forth sweetness. Do you know what that is? That's the riddle that Samson told the Philistines.'"

As a teenager, he began to question the beliefs he had grown up with. He learned science. "I learned that conception actually involves a man and a woman. I learned the age of the universe, that it couldn't really be created in six days. The traditional path of scepticism.

"It was partly rationality, it was also the sense that the universe was an empty place. Existentialism was in the air, a sense of the futility and meaninglessness of life, which appeals to you greatly at the age of about 15 or 16," he chuckles. "But anyway, the result was to leave me with the sense that if there was a God, he was so inconceivably far off and distant that he was out of reach, so I had better live as if there were no God.

"I did go through periods of a certain amount of anguish about this, but that's behind me now. I should think so at the age of 63."

I'm reminded of two things. The opening line of Julian Barnes's meditation on death, Nothing To Be Frightened Of: "I no longer believe in God, but I miss him," and Terry Pratchett, who once described himself as "the kind of old-fashioned atheist who's angry at God for not existing".

"That's a good line from Terry Pratchett. When Kingsley Amis was asked, 'Are you an atheist?' he said, 'Yes, but it's more that I hate him.' There's plenty to hate there, plenty to be angry with. The God who is depicted in the Old Testament is a peculiarly unpleasant psychopath. The Church, in whichever of its varieties, has done all manner of extraordinarily wicked things."

At the same time, he admits, it's more complicated than that. The Church has done good, too. It's with a sense of regret that he talks about how the Book of Common Prayer has fallen from use, along with his most beloved hymns.

"I have the feeling that the Church has left me, as much as I've left the Church.

"I respect the view of (cosmologist and astrophysicist] Lord Rees, who I think said that he's not a believer, but he'd like to be buried in an English country churchyard according to the rites of the Church of England. That's the sort of thing that appeals to me, though I don't suppose there's a churchyard that would be ready to take me."

One of the most moving passages in The Good Man Jesus and the Scoundrel Christ finds Jesus on his knees, crying out to a God in whom he no longer believes. Pullman says this voice is his. It's full of sadness, anger, a resolution to find in the ordinary, everyday world that which TS Eliot described as "something upon which to rejoice".

"Like this old dog, here," nudging the snoring pug gently with his foot, then murmuring an apology and laying a conciliatory hand on the old dog's back. "Can't see, can't hear, can't do anything except go to sleep. I envy his ability just to put his head down and enter the land of nod."

Although he has taken pains to explain his beliefs in rational terms, there is more to life than the pure rationality. Certainly, there is more for a writer like Pullman, capable of such flights of imagination as he is in his books, who writes so empathetically that he has been known to weep or laugh along with his characters.

Pullman started writing children's books in 1972, and gave up teaching to write full-time 14 years later, but he says the impulse for His Dark Materials came from a sense of despondency that he would never break through to the big time. "I had a freedom which came out of desperation. I was never going to make any money by writing realistic books, so I might as well write what I like.

"Because it was a children's book, I knew that nobody would take any notice of it, but that it would stay around for a few years, and maybe one or two adults would read it in the fullness of time. But it happened rather more quickly and more fully than I expected."

The three books have sold over seven million copies worldwide. The Amber Spyglass became the first children's book ever to win the Whitbread Prize. The trilogy was adapted by Nicholas Wright into an immensely successful stage play, and Northern Lights into a Hollywood film starring Nicole Kidman and Daniel Craig. Though denounced in some religious quarters, it gained support in others, not least from the Archbishop of Canterbury, who suggested it be studied in schools. Fans should note that a further title in the series, The Book of Dust, is in the pipeline.

While he is always careful to say that the books had no agenda, he is also happy to engage in ideological battles. "I think I knew what I was doing. But I had to go to these places. Why? Because the imagination wanted to go there."

He speaks of the imagination as an intuitive, headstrong "master", balanced by the rational mind as a "steady, sensible servant". "You have to shape what you've discovered into a satisfying story, by making patterns and correspondences and so on. By cheating, in other words, to make a better story out of it."

Which brings us back to Jesus, the intuitive storyteller par excellence. And then there's Christ, the one who shapes the story, writes it down. Christ is the one you've really got to watch. Christ is a writer.

• The Good Man Jesus and the Scoundrel Christ by Philip Pullman is published by Canongate, priced 14.99.