One day in 1951 while meditating beside the world's largest free-standing boulder in the Mojave desert, George van Tassel was transported aboard a spaceship orbiting the Earth. In the 50s, visiting aliens were not evil predatory Martians as envisaged in HG Wells's War of the Worlds, but all-wise Venusians who sought to improve us feeble Earthlings.

True, cosmologist Carl Sagan later showed that Venus was inhospitable to human-like life forms since its surface temperature seemed to be upwards of 600K (roughly the melting point of lead), but let's not spoil the story.

"These aliens were beautiful humans who wanted to give us the extraordinary secrets of wisdom and longer life," says Hari Kunzru, whose new novel Gods Without Men includes an acknowledgment to Van Tassel and has a character inspired by his life. "They thought we had the technology, but lacked the wisdom because we didn't live long enough."

When Van Tassel returned to the desert after his meeting with the Venusians' all-wise Council of Seven Lights, he set to work building a life-extension machine using his aeronautical engineering skills. He called it the Integratron, which may make you think of the Orgasmatron in Woody Allen's sci-fi comedy Sleeper, but it was nothing like that. "It was a huge coil that created potential and people could bathe in positive ions, or maybe it was negative ions, and in so doing repair their cells so they could live for 150 years and thus be old enough to gain wisdom," explains Kunzru. But Van Tassel never did get the Integratron to work. He died in 1978, leaving us no wiser nor longer lived.

More than 60 years later, Kunzru was on a road trip through eastern California when he stopped at a retreat at nearby Joshua Tree. It was there he came upon the story of Van Tassel.

In Gods Without Men, Van Tassel becomes Schmidt, a contactee, ufologist and founder of a cult. Kunzru's almost self-defeatingly ambitious fourth novel is about the human quest for transcendence – not just encountering big-brained Venusians, but the hope of finding a thing that sometimes goes by the name of God. It time shifts virtuosically from an 18th-century Spanish mission and its attempt to Christianise the indigenous population, an alien-fetishising cult in the shadow of the cold war, a countercultural 60s encampment, right up to a contemporary drama of a four-year-old autistic boy who disappears inexplicably into the desert wilderness, leaving his parents bereft and bewildered.

Kunzru has always been an ambitious novelist. His first novel The Impressionist was a clamorous baggy monster of a debut with a protagonist who shape-shifted like a postmodern version of Kipling's Kim from rich Anglo-Indian kid at the time of the Raj to English gentleman and then to explorer of Africa.

The story in that debut, though, was eclipsed by the backstory of how Kunzru had received a £1.25m two-book deal from Penguin after presenting it with the manuscript. Many read The Impressionist; many more read – with mounting bile and envy – about how the then 31-year-old, hitherto impecunious journalist had got one of the most lucrative book contracts ever. "I was well paid for The Impressionist and that helped me to focus on writing novels rather than accepting every journalistic commission," says the public school- and Oxford-educated millionaire. "But the coverage made it sound as though I'd become Puff Daddy overnight." Instead of filling swimming pools with Cristal and hotties of both genders, though, he bought "a rather nice house" near Victoria Park in east London.

Kunzru was so enviably successful that he could turn down awards. Yes, he accepted the Betty Trask and Somerset Maugham awards for The Impressionist, but he turned down the 2003 John Llewellyn Rhys prize because it was sponsored by the Mail on Sunday. He said in a statement: "As the child of an immigrant, I am only too aware of the poisonous effect of the Mail's editorial line. The atmosphere of prejudice it fosters translates into violence and I have no wish to profit from it." Not only did Kunzru turn down an award, but he did so out of unimpeachably noble principle, damn him.

Worse yet, his second book was just as good as the first. In Transmission (2005), Kunzru channelled the techie sensibility he had acquired working at Wired magazine. He capitalised astutely on the then voguish themes of computer hackery and the dotcom bubble in a satirical work about an Indian computer programming geek who concocts a virus so sinister only he will be able to cure it – thus making him an indispensable employee. But when, as a result, computer systems around the globe suddenly become inoperable, he becomes not indispensable but the world's most wanted terrorist.

Kunzru's third novel, My Revolutions (2007), was equally topical, exploring extremist politics in a story ostensibly about communist revolutionary terrorists in London in the late 1960s and early 70s but with resonances for present day Islamic fundamentalism.

None of these three books would have led one to expect that Kunzru would go way out west for his fourth. "I don't think it's that unpredictable," he counters. "By being a European interested in the American desert I'm following a tradition. Think of Wim Wenders's Paris, Texas or how the French have Lucky Luke."

But the European whose desert experiences most resonate for Kunzru were those of British architecture writer Reyner Banham. "In Scenes in America Deserta, Banham wrote about ruined deco motels and the sense of emptiness from an English perspective. He wrote that the most epic landscape he knew before the Mojave was Mousehold Heath in Norfolk, which I thought was amusing, and certainly resonated for someone from Essex like me.

"When friends from LA go to the desert, they want to sit in hot tubs listening to Gram Parsons [surely a defensible spiritual quest, since the singer-songwriter died in a Joshua Tree hotel room in 1973], while Europeans like me go there to get into cosmic relation with the void."

Kunzru first stumbled across the US desert landscape 10 years ago this coming September. "I was supposed to fly home from LA on 12 September, but they said the next flight would be in eight or nine days. People were behaving in this really unpleasant, hyper-nationalistic way – so I got away. I decided to drive to Vegas and think about what had happened. I stopped at Death Valley, which seemed appropriate.

"When I arrived in Vegas, it was so strange – they were trying to do grief. There was a New York, New York casino which became a focus. I was the only person at the Aladdin diner opposite, sitting there with a beard feeling conspicuous."

But that excursion kindled a love for similar desert road trips. "Since then I've become the king of the $40 motel room," he recalls over coffee beneath leaden London summer skies in Covent Garden. During his travels he visited mission churches, casinos for low rollers, dying towns at the end of abandoned railroads, eccentrics who retreated to the wilderness to paint mountains with slogans expressing their "God is love" theology.

These experiences fed into his multi-layered novel, some of which he wrote in hotel and motel rooms in California, Utah, Arizona and Nevada. "Some people find deserts frightening and empty, but I would rather walk a mountain ridge or a desert than a forest." You go on your own? "Sometimes. I can do a lot of not speaking. I'm pretty happy on my own."

For the past three years he has lived in Manhattan's East Village, which intensified his fondness for desert tripping. "New York is so vertical it's psychologically relieving to be somewhere so horizontally extended. I like to rest my eyes on the void."

But the desert of Gods without Men is hardly a void. The fruits of this imagined wilderness are so rich that one wonders why so few novelists have set their books there. Kunzru uses the desert locale to explore indigenous myth systems, Catholic missionary culture, the transcendental Tibetan Buddhist concept of the bardo or state of existence intermediate between two lives on earth, and – in one bravura sequence – how the military prepare for war. He imagines a Baudrillardian war simulation exercise in which Iraqi refugees are paid to play the roles of Iraqi villagers so GIs can ready themselves for the real thing. The insurgents – nice touch this – are played by American soldiers.

It was in the Mojave desert that the Mormons saw a tree called the Yucca brevifolia, which they called the Joshua Tree since its shape reminded them of Joshua reaching his hands up to the sky in prayer. In Kunzru's novel, a desert rock formation called the Pinnacles has a similar symbolic function: its trinitarian structure leads characters in the novel to impute to the desert a Christian significance. It is in the desert that the very rocks and trees point us away from diabolical temptation and towards God – if we are of a temperament to read their messages.

Kunzru is surprisingly sympathetic to such transcendent sensibilities given he has no faith. "I'm not a member of organised religion and I wouldn't say I believe in anything that you could hang the name 'god' [on] but transcendence is clearly important in what it is to be human."

His father, Ravi, a Kashmiri descendant of Hindu Brahmins, is an orthopaedic surgeon whom Kunzru portrays as a man of science sceptical of organised religion. His mother, Hilary, an Englishwoman raised as a non-conformist Christian, worked as a nurse. "[My father is] a scientist and dislikes ritual of all kinds, but will go along with some of it for the sake of his sisters. My mother, I think, is now agnostic – she resents the authoritarianism of her upbringing."

Little Hari, born in 1969 and raised in Woodford, Essex, fell between the two stools of his religious heritages: "The decision was taken that I would neither be baptised nor given the sacred thread [ie, the Hindu ceremony of Upanaya]."

Kunzru personifies the conflict between faith and reason in a story he weaves through his latest novel of how a father and mother deal with the disappearance of their four-year-old autistic son, Raj Matharu, during a trip through the desert. The father, Jaz, is a Sikh American of Punjabi ancestry and a maths whizz whose skills prove valuable to track fluctuations on the bond market when he is hired by an innovative, if venal-sounding, Wall Street hedge fund. The mother, Lisa, is a Jewish-American publisher lured from her secular worldview into making a leap of faith to something like religion by the traumatic impact of both her son's autism and his disappearance.

Kunzru says of the couple: "He wants to predict and control. He's an information-driven creature. Hers is the magical thinking that if you believe something, it will transpire." It's not the Matharus' only clash. There is a row when Lisa wants their son be circumcised. "If I didn't do this for him," she says, "They'd have won. All those bastards who wanted us to disappear." Jaz retorts: "And what about my culture? . . . The Muslims tried to convert us by force. They tried to circumcise us by force. Do you understand?"

I tell Kunzru I fund this passage fascinating because, in it, both parties are ostensibly secular, but as soon as rearing a child gets serious, they revert atavistically to Sikh and Jew. "I don't have children yet, but I notice when people have children they have to face up to the possibility that they may have to find a role for their ancestral tradition even if that means they endorse cultural or religious practices for their child they would have earlier despised." Kunzru lives with his Japanese-American novelist girlfriend Katie Kitamura, so heaven knows what kind of cultural differences they may have to work through if they have kids.

The Matharus' struggle with their son's autism is poignant but his disappearance will doubtless have some readers comparing their travails with those of Kate and Gerry McCann, particularly when the online bile merchants chide the traumatised Matharus for being cold and aloof, and for not performing their grief in public sufficiently gaudily. The couple get blamed for the abduction, spat at in the street, accused of paedophilia and subjected to a media witch-hunt.

It is a story whose poignancy and momentum is undermined by Kunzru's very virtuosity in switching back and forth between time zones, like a Doctor Who of fiction insufferably keen to show his mastery of the new Tardis.

Near the novel's end, Lisa reflects on how the experience of that witch-hunt changed her view of the world. Now she sees that skein of civilisation as thin, one torn apart by the inexplicable disappearance of her son and her fellow humans' toxic reaction to it. Kunzru describes the blogosphere flaming that the couple suffer as being fuelled by fear of the unknown. "Their fear made them dangerous, murderous even for in their blind panic they'd turn on whoever they could find as a scapegoat, would tear them into pieces to preserve this cherished fiction, the fiction of the essential comprehensibility of the world."

It is the novel's key passage, expressing God without Men's great theme. "I'm interested in the unknown and the unknowable and the role they have in our understanding," says Kunzru. And perhaps how irrationalism and faith thrive in such conditions. Throughout he seems to be arguing that the quest for meaning is a human projection on to the void. In a novelistic echo of the German philosopher Ludwig Feuerbach, Kunzru suggests that religion – especially Christianity – is best understood as a projection of human longing.

In the middle of all these storylines, Kunzru finds a way of working in the financial meltdown as Jaz's Wall Street wheeler dealing goes hideously awry. Kunzru is torn about speculative finance, finding it intellectually thrilling and socially disgusting. "I think how the high priests of abstraction work is fascinating. I'm really interested, for instance, in a postwar Wall Street speculator called WD Gann who used astrological techniques. The idea of predicting and controlling is quixotic. It's all about the will to believe.

"This stuff is cool, but also hideous. What's happened since 2008 is a class war based on faith and credit, a fantastic con trick by the ruling class to immiserate the poor further while concentrating wealth more than ever in the hands of the rich. I'm not a Marxist but I'm more left-leaning than before I lived in New York."

Why? "Healthcare! If I have a message for people in Britain, it is that the NHS is incredible. Anybody who tries to fuck around with it in terms of marketisation should be ignored. What they have over there is terrifying. A friend of mine fell down in the gym. The gym rang for an ambulance and she said, 'Please tell them not to come,' because it would have been so expensive. Another musician friend set his own bones using information from the internet. It's totally dysfunctional.

"Why do I live in New York? Because it's like the desert, it's a fascinating place to be. I'm not growing old there, though."

• Gods Without Men is published by Hamish Hamilton, £12.99. To order a copy for £9.99 with free UK p&p, go to theguardian.com/bookshop or call 0330 333 6846.