“All of my books are about power,” Robert Harris acknowledged in a recent interview. While that power is most often political – the fall of a charismatic former prime minister in The Ghost, Chamberlain’s struggle for peace in Munich, the failure of the Roman republic in his wonderful Cicero trilogy – he has explored its perils in other, more insidious guises: technology in The Fear Index, religion in Conclave, the devastating force of nature in Pompeii. What connects them all is a preoccupation with power at its overweening apogee, on the brink of combustion and collapse. Charged always with contemporary resonance, it is a fascination that in his best books comes unsettlingly close to prescience.

The Second Sleep is driven by the same preoccupation. Described as a “genre-bending thriller”, it appears to open conventionally enough “late on the afternoon of Tuesday the ninth of April in the Year of our Risen Lord 1468”. A young cleric, Christopher Fairfax, is making his way resentfully to a remote corner of Wessex on the orders of his bishop to officiate at the burial of a village priest. An hour’s ride past a market town where “three executed felons hung rotting from their gibbets”, his aged horse sliding on the muddy road, he is afraid that he has been misdirected; that he will be caught out of doors after curfew, risking a night in jail. By the time he finally reaches his destination, he is determined to conclude his unpleasant business as swiftly as he is able.

In his opening pages Harris conjures a lost England in its mix of religiosity and brutishness. There are moments when the details feel off – a parakeet flashes through the darkness, surely an anachronism? Were there really longcase clocks in the 15th century? – but it is only when Fairfax discovers a display cabinet in the dead priest’s study, its shelves crammed with illegal artefacts, that the truth of this world is revealed. Among the plastic bottles, banknotes and toy bricks displayed there, Fairfax discovers “one of the devices used by the ancients to communicate”, its back marked with the ultimate symbol of their “hubris and blasphemy – an apple with a bite taken out of it”.

Facebook Twitter Pinterest Robert Harris. Photograph: David Levene/The Guardian

It is a stunning sleight of hand. Abruptly everything shifts, slotting those strange anachronisms into place. Fairfax’s 15th century is not ours but part of a new calendar that had been reset to 666, the numeral of the Beast of Revelation. In Harris’s imagined future, God has brought down the four riders of the apocalypse on the satanic civilisation of the 21st century and the church has reasserted itself at the centre of the state. “Scientism”, the curse of the ancients, is a heresy, a mortal sin. Stripped of the medical and technological advances of the Industrial Revolution, life is once more nasty, brutish and short. It has never occurred to Fairfax to question the principles that underpin this world order but, in this remote rural backwater, he stumbles on books and papers that challenge his most fundamental beliefs. Though it is a crime to investigate the past, over the days that follow he finds himself drawn ever deeper into a quest to discover the truth.

During the course of his career Harris has perfected the art of creating tension within a story to which we already know the ending: the Enigma codes were cracked, the eruption of Vesuvius destroyed Pompeii, the Munich Agreement did not bring peace. In The Second Sleep he turns the tables: this time we do not know the beginning. Twenty-first century civilisation has crashed to a catastrophic end – but why? Was it technological failure, antibiotic resistance, nuclear war? The stage seems set for a classic Harris thriller, the lowly functionary intent on challenging the entrenched interests of a secretive and ruthless state.

Instead The Second Sleep develops into something more contemplative: an exploration of a world that is both unfamiliar and as old as time, and of the consequences of our flagrant disregard for the existential perils of our own era. A convincingly imagined future world requires a steady accretion of small, telling details and there are sections in Harris’s novel that feel frustratingly inconsistent or approximate. But if his dystopia lacks the political and social coherence of, say, Gilead in The Handmaid’s Tale, he has contrived in The Second Sleep to do something rather brilliant and new. He has put us at the heart of the mystery. Whatever disaster has struck the world it has struck because of us, our greed and ambition, our arrogance. We are all responsible. As Fairfax edges closer to the truth, the reader is left with at least as many questions as answers, and most of those questions are directed at ourselves.

• Clare Clark’s In the Full Light of the Sun is published by Virago. The Second Sleep is published by Hutchinson (£20). To order a copy go to guardianbookshop.com or call 0330 333 6846. Free UK p&p over £15, online orders only. Phone orders min p&p of £1.99.