The historical novel, so that its period setting may be a source of illumination and enjoyment rather than confusion and tedium, is more or less bound to make a sop to the reader. Henry James, in his unfinished novel The Sense of the Past, chose as his main character a present-day historian who, when he crossed a certain threshold, was transported to the age of Byron; Dickens, portraying pre-revolutionary France in A Tale of Two Cities, approached the period in an antiquarian spirit ("It was the best of times, it was the worst of times"), and used English characters who would function as proxy-eyeballs for an English readership.

Andrew Miller, treating the same period in his accomplished new novel, gets by without such crutches. He drops us right into Paris in the last days of the ancien regime, a place of contagion and contamination where Miller's young hero, engineer Jean-Baptiste Barratte, has come to lose his illusions and find his fortune. Miller uses a varied French cast, none of whom is an avatar of, or spokesman for, the 21st century. When characters talk of the "future" or "modernity", they are looking forward only a few years, to the era of Danton, Robespierre, and Napoleon  though the reader is never prompted to cry: "Look ahead of you!"

Jean-Baptiste, usually identified as "the engineer", arrives in Paris from Normandy and is immediately given a mission. Louis XVI long ago ordered the closure of a church, Les Innocents, and its pestilential, overflowing cemetery. Now, one of the king's ministers tells the engineer, it is time for it to be made "sweet again": "Decent, habitable. Pure." The minister fails to realise that such an act will be received by many as a step towards a necessary purification of France, as carried out by her citizens. The engineer, a follower of Voltaire and Diderot, thinks of it as sweeping away "in fact, not in rhetoric, the poisonous influence of the past". But it soon emerges that those who have become accustomed to the stench of human dust are less than enthusiastic about the engineer's project.

Although Miller has resisted using English characters or a well-informed narrator, the engineer does represent an outsider type of a familiar, perhaps too familiar kind. As defined by Lionel Trilling, the Young Man from the Provinces "starts with a great demand upon life and a great wonder about its complexity and promise"; he is intelligent but not shrewd; he has learned "something about life from books, although not the truth"; he "stands outside life and seeks to enter". The engineer has all of these properties and undergoes the customary processes, as if on cue. And when his new friend Armand, the organist at Les Innocents, introduces him to Paris  to its inns, fromageries, and tailors  the reader is there with him, taking mental notes.

It is disappointing, given the vitality of the novel's setting and set-up, that Miller fails to achieve corresponding dynamism in the development of plot and character. The destruction of Les Innocents consumes the novel, from first line to last, but the consequences of the project are never made to matter to the reader as much as they matter to the engineer; the dark results are not dark enough. As a prose writer, Miller appears averse to taking risks, which means no pratfalls  but no glory either. The engineer's progress and his setbacks are narrated in a patient, tight-lipped present tense, and just as the novel rarely concerns itself with anything that doesn't impinge on the destruction of Les Innocents, so it rarely deviates from its obsessive regime of description and dialogue.

Henry James, having failed to complete The Sense of the Past, became convinced that the historical novel was a doomed enterprise; it could replicate facts but would fail to represent a consciousness "intensely-otherwise conditioned". Miller exposes the folly of James's distinction between facts and consciousness. He succeeds in representing the consciousness of his characters by scrupulously selecting which facts they will be familiar with and which they will find unsettling or strange. It is one of the historical novel's advantages over the topical or journalistic novel that the benchmark is plausibility rather than verifiable authenticity. Success in this effort requires a capacity for immersion and a degree of imagination, and whatever his shortcomings as a prose writer and a storyteller, Andrew Miller is endowed with both.

France, in the turbulent years before the revolution. At Versailles a minister in Louis XVI's government tells a young engineer that there is an elephant somewhere in the palace. A gift to Louis XV from the King of Siam, it lives on burgundy wine and must be kept hidden away for fear that the palace dogs, once terrified of the great beast, might now set upon it and kill it. From the portentousness with which the minister weighs his words, the engineer thinks that the animals might almost be "figures in a parable".

It is an audacious novelist who can so knowingly prefigure the symbolism at the heart of his own work without threatening the success of the entire enterprise. It is fortunate, then, that Miller is a writer of subtlety and skill. Pure, his sixth novel, goes on to tell the engineer's story. A young man of humble background, Jean-Baptiste Baratte is ordered to exhume the vast and ancient cemetery of Les Innocents in the poor Parisian quarter of Les Halles and demolish its church. No one knows how many bodies are buried there  it is claimed that during one outbreak of the plague the graveyard received 50,000 in less than a month  but it has recently begun to burst its banks, poisoning the city and spreading "moral disturbance". Baratte's hiring is inadvertent  he is at first mistaken for someone else  but it is to herald the beginning of a year "unlike any other he has lived".

Baratte finds that the stink of the dead dominates the quarter, fouling the air and tainting even the breath of those who live there. The vast smoke-blackened church that presides over the graveyard obliterates the light. And yet, as the engineer begins his grisly excavations, he finds that the residents of this poor and labyrinthine district have a powerful attachment to both. There are also those who support his work, among them a kindly doctor, Guillotin.

Miller's parable is unambiguous. As Baratte's story unfolds, the impending revolution hangs over the narrative like the blade of the guillotine to come. Jean-Baptiste Baratte, or John the Baptist the Churn, is in Paris to prepare the people for the coming of the true messiah. It is his duty to rip away the filth of the past, to lay the foundations for a new, better world. As his foreman declares: "They will name squares after us . . . the men who purified Paris." Everywhere there are auguries of the turmoil to come: an organist plays to an empty church, the local theatre stages Beaumarchais's revolutionary Marriage of Figaro, a cart rumbles round the quarter, its side emblazoned with the legend "M Hulot et Fils: Déménageurs à la Noblesse".

Meanwhile, the half-disinterred cemetery becomes a kind of hell, with huge fires kept burning day and night to clear the air. Bones are piled in heaps. The brutish miners brought in to clear the corpses collapse inexplicably in the deep pits. Prostitutes shriek in the shadows. There are acts of madness, unexplained violence. As the foreman of works observes bleakly: "I had some good in me once."

Unlike many parables, however, Pure is neither laboured nor leaden. Miller writes like a poet, with a deceptive simplicity  his sentences and images are intense distillations, conjuring the fleeting details of existence with clarity. He is also a very humane writer, whose philosophy is tempered always with an understanding of the flaws and failings of ordinary people. He does not deal in heroes. Baratte takes a determinedly scientific view of the world  his nightly catechism is not a prayer but an assertion of the "power of reason"  but in the end his science does not comfort him. He is an accidental protagonist, a man riddled with self-doubt who purchases a pistachio-green silk suit because it is modern but who never feels comfortable wearing it, who reads the latest books but ends up using their pages as toilet paper.

Pure defies the ordinary conventions of storytelling, slipping dream-like between lucidity and a kind of abstracted elusiveness. The characters are often opaque. The narrative lacks dramatic structure, unfolding in the present tense much as life does, without clear shape or climax. It is left to us, who know the world that came after, to impose upon Miller's tale the weight not only of the revolution that would tear France apart but also of the war-torn centuries since, the twinned history of progress and bloodshed. The result is a book that is unsettling and, ultimately, optimistic. Flowers bloom again in the disinterred cemetery. Sunlight illuminates the darkness through the broken roof of the church. Though progress brings suffering and death, the balance, as Baratte knows, "will still be in your favour". As Miller proves with this dazzling novel, it is not certainty we need but courage, now as much as ever, before we too are reduced to bones.

Clare Clark's latest novel is Savage Lands (Vintage).