When, in 1997, Christianity Today, the flagship magazine of American evangelicalism, decided to pay tribute to the late Francis Schaeffer, the theologian and popular writer must have seemed like an odd choice to those not familiar with the twists and turns of the evangelical world. Most of Schaeffer's work and life was at sharp odds with American-style evangelicalism.

Raised in Pennsylvania, Schaeffer lived much of his life as an expatriate in a Swiss chalet. His early books in the 1960s struck out against American evangelicalism's know-nothingism. When he lectured in the US, he would discuss the films of Bergman and Fellini on Christian campuses that wouldn't allow screenings of Bambi. He welcomed seekers from all faiths at his Swiss retreat, and didn't worry about the baggage they brought with them. "Backpacking private pharmacies," as Frank Schaeffer, son of Francis, characterises his father's disciples. L'Abri (or "the shelter"), as his father called the home they opened to all-comers, was in the 1960s and 1970s - the height of Schaeffer's intellectual production - a place of blasting music at all hours, drugs, sex and rock'n'roll. When a young Frank Schaeffer happened to meet Jimmy Page in 1969, Led Zeppelin's guitarist pulled a copy of one of Schaeffer Sr's early books, Escape From Reason, from his pocket and declared it "very cool". He said Clapton had given it to him.

And yet here Schaeffer was, filling pages in Christianity Today. To make the case for his relevance, the magazine noted the heirs to his legacy, the men who had carried his counter cultural theology into the world: among them Jerry Falwell; Pat Robertson; Randall Terry, founder of the militant anti-abortion crusade Operation Rescue; and Tim LaHaye, founder of the ultra-right Council for National Policy and co-author of the Left Behind series of apocalyptic novels that have sold 65 million copies around the world. These men claimed Schaeffer not just as a major influence, but as one of the most important thinkers of conservative evangelicalism of the 20th century. Indeed, one of its only "thinkers": Christian right leaders have long been aware of their movement's relative lack of gravitas. "From the mid-1970s until he died," recalls Frank, "Dad was drafted . . . by the Missouri Synod Lutherans, Southern Baptists and other conservative denominations as a kind of intellectual heavy-gun-for-hire."

What happened? How did Francis Schaeffer's work go from Jimmy Page's back pocket to the hate-filled pulp of LaHaye, the spittle of Falwell? In 1969, Eric Clapton recorded a song called "Do What You Like" with a band called Blind Faith; almost three decades later, another Schaeffer fan, James Kopp, with Schaeffer's ideas swirling around his head in a toxic stew of bad theology, shot an abortion provider, Dr Barnett Slepian, to death. Who got Schaeffer wrong? The hippies who flocked to L'Abri, or Falwell? Clapton, or Kopp?

That question haunts Frank Schaeffer's new memoir of being Francis Schaeffer's son, Crazy for God: How I Grew Up As One of the Elect, Helped Found the Religious Right and Lived to Take All (or Almost All) of It Back. (My pre-publication copy sports a blunter subtitle: How I Helped Found the Religious Right and Ruin America.) It's a brilliant book, a portrait of fun damentalism painted in broad strokes with streaks of nuance, the twinned coming-of-age story of Frank and the Christian right. But this story moves in more than one direction: both coming-of-age narratives are pulled against the current by the tragedy of Francis Schaeffer, a man who let his children, biological and ideo logical, guide him down a path from which he'd spent his whole life struggling to get off.

"Fran" Schaeffer grew up working-class in Germantown, Pennsylvania, a short, muscular boy abandoned by his father at age 12, berated by his mother his whole life, and born again in a tent revival at age 17. Schaeffer was a fighter in spirit as well as in fact, and he quickly took to the most belligerent expressions of his new faith. He met his wife, Edith, when he impressed her by standing up in a church to challenge a preacher who didn't hew to the doctrine of absolute biblical inerrancy. It was Edith who persuaded Fran to apprentice himself to J Gresham Machen, one of the early theorists of modern fundamentalism - a choice that would thereafter direct Fran's considerable intellectual talents toward the defence of a faith at war with itself, as American Protestantism split into warring camps, not just fun damentalist and liberal, but endless varieties of fundamentalism, each sniping at the other.

"My father's theology was formed in a particularly bitter moment," writes Frank, "and never evolved with the rest of his thinking. The theological battles of the 1920s and 1930s shaped Dad in the same way that political battles would shape the Vietnam generation in the 1960s." And yet, if Francis Schaeffer's theology did not grow, his "world-view", as he called it, certainly expanded. He read widely across philosophy, literature and history, hungered for new music and old, and, most of all, fell in love with art.

"Dad had one big idea: God has revealed himself to us through the Bible. And he spent a lifetime trying to fit everything into that one idea, and explain away anything that didn't fit." Schaeffer tried to convince himself that his love of art was in service to this one big idea. "Instead of spouting Bible verses," Frank writes, explaining his father's appeal to hippies, freaks and would-be intellectuals allergic to old-school fundamentalism, "Dad talked about philosophy, art and culture. Only when he had gained his listener's interest would he slip in a more traditional 'Jesus Saves' message."

The impact of this technique on American religion - and, consequently, the politics of the US and thus the world - can hardly be overestimated. Evangelicals were savvy to marketing long before Francis Schaeffer came along, but he taught a generation of evangelical leaders to engage "the culture" - it's a singular beast, in their imaginations - as fully as possible, the better to conquer it. Schaeffer was writing at a time when a different branch of elite evangelicals were self-consciously emulating what they understood of communist revolutionary techniques, "boring from within", "infiltrating" Establishment power. Schaeffer's approach was the subtler and, ultimately, more successful, heir - though he wouldn't like to think it - to the syncretic religion promoted by Roman Catholic missionaries, who around the world merged their saints with local systems of belief so seamlessly that conquest by the sword wasn't necessary. Schaeffer's similar strategy of cultural engagement explains why, after the age of Falwell and the collapse of George W Bush, evangelicalism remains influential, even if its old Republican patrons do not; one need only review the God-talk of the new Democratic candidates for president to hear echoes of Schaeffer's philosophy: the call for a "spiritual" solution to "material" problems, the acknowledgement of capitalism's awful limits unaccompanied by any systemic challenge to its predations.

The tragedy of Francis Schaeffer is that, at some deep inner level, he knew what he preached was a con. In 1967, he took his son Frank to Italy to share with him the art that he loved. "In theory, Dad was opposed to the 'humanism of the Renaissance' and was a champion of 'Northern European Reformation art', the works of the good Protestants. But in practice, it was the art of the Italian Renaissance that we spent much more time soaking up . . . In his L'Abri lectures, and later in his books, Dad would explain and even lament all this 'humanistic art' that placed 'man, not God, at the centre of the universe'. But when he was looking at the art with me, all we talked about was how beautiful it was, how remarkable." Standing before The Birth of Venus or Giotto's bell tower, Frank writes: "I saw Dad as he might have been, free of the crushing belief that God had 'called' him to save the world."

And yet it was Frank who reignited that belief in the mid-1970s, just as his father seemed finally to be shedding his fundamentalist leaves altogether. In 1972, a political evangelist named Billy Zeoli showed up at L'Abri to persuade Francis that with Zeoli's backer - the ultra-right Amway chieftain Richard DeVos - Francis could project his message far beyond L'Abri. Frank was even more tempted than his father; Zeoli was talking of movie-making, and the 20-year-old wanted in.

The result? Two series of films directed by Frank, How Should We Then Live? and Whatever Happened to the Human Race?, that are still shown in church basements to this day. Osten sibly created to allow Francis to connect his love of art with the fundamentalist gospel for a wide audience, the films became sacred texts of the anti-abortion movement. That was Frank's doing - Francis at first considered abortion a "Catholic issue", but his son persuaded him that it merited an all-out culture war, a battle Frank would fight for years before realising that, just because his fury over the issue was personal, it didn't have to be political. Yet long before then, his father had slipped so completely back to his fundamentalist roots that in 1981 he published the bestselling Christian Manifesto, a central text for the modern movement that trumpeted the belligerent Christian nationalism that Francis had once disdained.

And the art? The most succinct illustration of the clash between the Schaefferism that could have been, and the fundamentalism that instead fed and grew on his work, occurred when Billy Zeoli told the Schaeffers they had to cut some footage from How Should We Then Live?. Frank had put his father on some scaffolding next to Michelangelo's David to give a sense of scale, and the senior Schaeffer, high above the ground, close to the art he loved, had been transported into a distinctly unfundamentalist rhapsody. But that wasn't Zeoli's problem. He wasn't concerned with ideas. It was David's exposed genitals. American evangelicals, he said, just weren't ready for that.

Frank pointed out that they'd included footage of Mary's breast in depictions of the Virgin and the Baby Jesus. "One holy tit is OK," Zeoli responded. "But churches don't do cock!"

The senior Schaeffer gave in, muttering his dissent: "We're working with fools."

Jeff Sharlet is a contributing editor of Rolling Stone magazine. His book The Family: The Secret Fundamentalism at the Heart of American Power will be published by HarperCollins in April 2008.

Crazy for God: How I Grew Up As One of the Elect, Helped Found the Religious Right and Lived to Take All (or Almost All) of It Back, Frank Schaeffer, Da Capo Press, 304pp, £15.99