Episodes from an itinerant childhood still haunt him. Audrey remarried, the family moved to Australia and Pullman remembers his stepfather, also an R.A.F. pilot, once driving them “to a spot from which we could see one of the flooded rivers. I still remember this immense gray mass, sweeping inexorably from one side to another. There was no possible way of going against it or fighting with it. I was just aghast and thunderstruck by the power of this thing. So that’s always been with me.”

The family returned to Britain by ship and moved deep into rural Wales. Pullman’s youngest half brother, Mark, recalled the walks the children would take across the Welsh hills, during which Pullman would offer entertainment. “He’d tell us stories of things he’d read,” Mark recalled. “He’d tell us myths. He was studying Anglo-Saxon languages, and he’d tell us stories about that. There were always stories.” But at home, he was an outlier. “My parents weren’t literary people,” Pullman said, “in the sense of being passionately interested in books.” They read, but not the way he did, as if it were all that mattered. In Wales, he developed a committed relationship with a mobile library and is still grateful enough to the woman in the village who let him borrow her books to pay her homage in “La Belle Sauvage.” Dr. Hannah Relf lends the trilogy’s new hero, Malcolm Polstead, a classic Pullman reading list: Stephen Hawking’s “A Brief History of Time,” Agatha Christie’s “The Body in the Library” and a history of the Silk Road.

Pullman remembers being the only pupil at his school to sit for the Oxford University exam, and he was granted a scholarship. “Which was delightful,” he said. “But they must have realized how wrong they were within five minutes of starting the first tutorial, I think. I wasn’t a scholar. I’m not that sort of intellectual.” He emerged three years later with a third-class degree, the school’s lowest, and became a teacher, which gave him both time to write and an audience. At Bishop Kirk middle school in Oxford, he wrote plays for his students and told them his versions of the “Odyssey” and the “Iliad.” “I told each story three times a week, and I taught for 12 years,” he said. “So I must have told each one 36 times. I have all the stories entirely clear in my head and can call them up whenever I want.”

The Greeks permeate his writing. Like Odysseus, his new hero, Malcolm, is on a self-appointed quest, fighting off enemies from his boat. (He’s also very unlike Odysseus, being 11 years old, ginger-haired and partial, like Pullman, to woodworking and meat pies.) “The Book of Dust” has other touchstones too: William Blake, the occult, ancient civilizations, East Asia and a eight-minute piece by Borodin called “In the Steppes of Central Asia.” Most of all, Edmund Spenser’s epic, 16th-century allegory, “The Faerie Queene.” Pullman copies the structure of “The Faerie Queene” — strange encounter after strange encounter — but thankfully not its style. When I admitted how I had struggled with the countless pages of archaic verse, Pullman shouted, gleeful, from his seat: “So did I! Couldn’t read it. Couldn’t read it at all until I was doing this.” His own novel is more readable, and earthier, locked into reality by character and geography, Malcolm and Oxford. In it, Lyra is 6 months old and being hunted by henchmen of the Magisterium. The action unfolds in Oxford, but an Oxford unrecognizable from its spire-crowded postcard form — the city is a damp and threatening place of inns and drunks and amiable nuns. For half the book they are all submerged in a catastrophic flood. Malcolm navigates the waters in his canoe and becomes Lyra’s chief protector. After a gentle start, the novel accelerates into an action thriller, with cameos from fairies and river gods. There are boat chases, hints at romance. It will be devoured.

For a man whose novels are restless, whose characters never stop traveling, Pullman leads a relatively static life. After the morning shift at his desk, he spends his afternoons either tending to the 800-odd trees he and Judith have planted in the fields behind their house or in his carpentry workshop, where he makes things like reading stands and chopsticks. Occasionally, he drives an elderly woman in the village to the library, and he goes to the cinema once a week with his publisher and close friend David Fickling and their wives. “I have the company of the people I’m writing about,” Pullman told me. “Jude and I are quite happy here with our hermitlike existence.”

Together, they have the silent rhythms of their almost 50-year marriage (they have two grown-up sons and four grandchildren). He makes the soup; she makes the bread. They listen to classical music and berate the government over lunch at the kitchen table. Judith — gray-haired, gentle-voiced, wry — gives the impression of someone who is particularly unfazed by her husband’s reputation and absorbed in her own projects. (All those trees.) Once when I visited in midsummer, she was simultaneously watching a tennis match on television while checking cricket scores on an iPad. Judith had been a teacher, too, and the pair share passionate views on what the education of children should involve — more imagination, fewer tests. She is essential to Pullman’s work — his first reader and “a truth teller,” Fickling said. “I’d defer to her.” As we ate lunch at their home, she recalled reading “Northern Lights” for the first time while sitting upstairs on their bed. When she finally got to the end — in one engrossed sitting — she sprinted down the stairs and out into the garden to find him, shouting, “This is it!”

“La Belle Sauvage” is dedicated to Judith and is, surely, the beginning of the end of Lyra’s world. When we met during the worst of Pullman’s illness, I wondered, guiltily, if he would ever finish it. He was midway through the second volume — Lyra was in the Levant, and she still had to get to Central Asia. “A long way to go,” said Pullman wearily at the time.