“Nothing is just anything,” says one of the characters towards the end of this new excursion into Philip Pullman’s wonderfully imagined parallel universe. In the earlier His Dark Materials trilogy, Pullman developed with increasing complexity the idea of “Dust” as something like the animating power of adult imagination. It is Dust that enables the working of the “alethiometer” – the truth-telling instrument that operates by the alignment of layers of images superimposed on each other, like a kind of mechanical I Ching (the comparison with the Chinese divination technique is explicitly made in the third of the earlier trilogy) or tarot pack.

When openings are cut between different universes – a major plot device in His Dark Materials – Dust leaks out, and the ecology of all the worlds involved is ruinously affected. We are shown how the search in the world of Pullman’s story for a better understanding of Dust is linked with the quest in our world for “dark matter” in the universe. It is not quite clear how this works, but it gives Pullman a cue for reminding readers that scientific inquiry pushes the boundaries of what we can say about the universe’s interconnections, even in our world.

Meanwhile, in the universe where His Dark Materials begins, Dust somehow works as a metaphor for the connectedness between humanity and its environment, for the positive embrace of limit and mortality, for what arrives into human life with the advent of sexual maturation, and so for the energy that finally solidifies the “daemon” – the spiritual/animal alter ego that accompanies each person in Pullman’s world – into its long-term shape. It is the power that is paradoxically released when the drifting, gloriously polymorphous possibilities of childhood are left behind and the world is embraced in its obstinate particularity.

We learned also in His Dark Materials that Dust is a matter of threat and anxiety for the theocratic tyrants who are tightening their grip on this world. It is a result of the Fall of Adam: Dust comes with self-awareness, and self-awareness brings the possibility of sin. Hence the central theme of the first book of the earlier trilogy, the attempt of the religious authorities to find a way to halt the advent of Dust into human life by separating children from their daemons before the daemons attain their final, adult form. Tyrannous authority seeks to deny or expunge the dangerous joy of adult self-knowledge, with all that this makes possible.

It is equally true that the enemies of this authority are seduced by the idea of breaking open barriers between worlds and so releasing untold levels of energy in the resulting flow of Dust. Pullman seems to be saying that both religious single-mindedness and its mirror image in scientific hubris are enemies of that passionate embrace of the sheer density and beauty of the material world that animates true imagining. “Dust loves matter,” we are told in His Dark Materials; and the adult human mind, absorbing itself gladly in the material environment, discovers the only transcendence that counts. This is anything but reductive. It is more a way of affirming the unity of matter and spirit, the penetration of mind in all things – hence Dust is what makes possible the intuitive clairvoyance needed to read the alethiometer.

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All this is probably a rather tiresomely abstract preface to the pleasures of reading Pullman’s new book. But the reader will need some sense of why and how Dust matters to the characters in Pullman’s world. He has said that the new planned trilogy, of which this book is the first, is not intended to be a prequel to His Dark Materials (he has described it as an “equel”). This story, though, is set just over a decade before the opening of the earlier trilogy: Lyra, the tough, affectionate and intuitive heroine of His Dark Materials, is a baby in this book, and the main thread of its plot has to do with her rescue from a near-apocalyptic flood by an unlikely duo, the 11-year-old Malcolm and the 15-year-old Alice. Navigating the waters of the flood in Malcolm’s canoe (the Belle Sauvage of the title), they seek to return Lyra to her father, Lord Asriel. She is already the target of the Church’s agents, who are aware of the prophecies that identify her as the potential destroyer of the power of the religious authorities.

The flight of Malcolm and Alice with Lyra is to escape not only the flood but the pursuit of a particularly sinister agent of the inquisitorial authorities, Bonneville. The story sketches something of the political background of Lyra’s England, with the power of the Consistorial Court of Discipline gradually intensifying its stranglehold on various institutions – including schools – and combating resistance from a handful of figures in public and private life, some of them linked in a spy network. Hannah Relf, whom we meet briefly in His Dark Materials as the elderly head of a women’s college, appears here as a younger academic working to decode the symbolic allusions and cross-references of the alethiometer, and as an active undercover agent of the anti-Church network.

The basic story is more straightforward than the first volume of the earlier trilogy, Northern Lights, with its astonishingly vivid array of settings and creatures; no ice fortresses and armoured bears here, no witches flying on their cloud-pine branches until near the book’s end – though the “Gyptian” (Roma) community features, and we meet a younger incarnation of the shrewd old Farder Coram. But what Pullman does is to lock together a simple adventure story – of a resourceful young boy facing risks and challenges in his little boat – with a resonant mythical underpinning: the murderous search for and miraculous rescue of the magical/holy/messianic child. Moses saved from Pharaoh by being set adrift in a basket on the river, Herod pursuing the infant Jesus – these are in the hinterland of Malcolm’s and Alice’s voyage.

The chemistry between the two children is to some extent a reworking of the relationship between Lyra and Will in His Dark Materials: a stolid and serious boy, burdened with a sense of responsibility beyond his years, and a more mercurial and bloody-minded girl, gradually coming to feel deep affection for each other. At the end, Alice springs to Malcolm’s defence, swearing and spitting, when Asriel is angry with him: “If I told you the half of what Mal’s done to keep us alive and safe, well you wouldn’t imagine it could be true. You couldn’t dream of it… So take that f***ing smile off your face, you.”

This again is a transcription of an older legendary theme – the Arthurian trope of the knight being tested by having to accompany and protect an ungrateful and scornful lady, as in the tale of Sir Gareth in Malory. Pullman skilfully pitches these long narrative echoes without making them too obvious.

One of the most successful aspects of the story is the way that it traces the evolution of the children’s mutual respect, and their clumsy but remarkably effective nursing of the baby Lyra is described with credible – and loving – detail. But, as in His Dark Materials, there is a certain amount of fuzziness in focus around the age of the children: it is necessary for aspects of the plot that they are prepubescent (their daemons are as yet unfixed), but the Will-Lyra relationship is given a strong erotic charge in the third book of the trilogy, with an adult intensity and depth, though they are not more than about 12.

This is not quite such a problem here, but Alice’s age seems rather fluid. She narrowly escapes being sexually assaulted by the appalling Bonneville and seems to react to this as a fairly self-conscious teenager rather than simply a child, yet she still has a non-settled daemon. Pullman negotiates all this without too much jarring, but the awkwardness is inescapable. It does, however, allow Malcolm some believable motivation when, in a disturbing episode, he frenziedly attacks Bonneville after seeing him attempting to rape Alice.

The darkness of this strand of the story is intensified further by the depiction of Bonneville’s private tortures. Malcolm witnesses him beating and abusing his own (hyena-formed) daemon: “The terrible fury of the man came after her, thrashing and beating her with his stick, and the frenzied laugh-like agony filled the air.” This is, in Lyra’s world, an unthinkable act both of self-harm and of violation, and it surrounds Bonneville with an air of extreme, sick perversity.

For much of the book, the narrative energy keeps up well: Pullman’s style is lively and physically specific, and the descriptions of the flood and its consequences are brilliantly done. But I was puzzled by the way in which the second part seemed artificially lengthened by two chapters that didn’t appear to contribute anything to the flow of the story, one involving a visit to an “enchanted island” (with echoes of Alan Garner and of Tolkien in the idea of a respite in the journey thanks to an elvish princess), the other an episode in a country house inhabited by ghosts of a kind never quite explained. It may be that future volumes will shed some light; but in terms of this book, it felt (uncharacteristically) like padding. As in some passages of the third volume in the earlier trilogy, sheer invention without sufficient root in the demands of the story makes the narrative sag – and also makes the concluding pages feel somewhat rushed.

How, then, does the story bear on the question of the nature of Dust? Pullman implies that the crisis focused on the birth of Lyra and the Church’s panicked response to this is what prompts the heavy rain and subsequent flood. As in His Dark Materials, there is a link between the malfunction of mind and the corruption and disturbance of the material world, and a novel dominated by a flood of epic proportions is clearly meant to introduce a story – as Lyra’s story will turn out to be – of spiritual violence and distorted desire, rebellion not against God but against the hard truth of mortality. Lyra in the earlier trilogy turns out to be an apostle of this hard truth and a revealer of its surprising joys. It is appropriate that her baby­hood is marked by the signs of panic in an institution devoted (in Pullman’s eyes) to the denial of mortality and by the upheaval of an ecology disturbed by that denial.

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It was an odd experience reading this book as images of catastrophic flooding in Asia and America filled television screens and newspaper front pages. One of the many ways we can read Pullman is as a story­teller who wants to persuade us to start attending again to the connections that we have lost the ability to see – because connections that are unseen will still work out their consequences. We may tell ourselves till the cows come home that our human destiny is not really bound up with the delicate material ecology we inhabit, but the results of human greed and stupidity will be what they will be, whatever fables we make up.

If the recital of facts will not change us, perhaps fiction will – fiction that begins with the need to imagine who we are in relation to what we think we are not. Pullman is, in this way, an intensely “spiritual” writer – if by “spirit” we mean the awareness of our connectedness in and through the material stuff that we are. His often vitriolic pictures of religion are premised on the assumption that its most familiar traditional forms are necessarily committed to battling against Dust, against what I earlier called the adult imagination.

This book does at least find room for some kind and courageous – and far from stupid – nuns; but Pullman’s Consistorial Court reflects not only the Inquisition but the techniques of the Third Reich (societies for children that encourage them to spy on and denounce their families), and one of the two convents depicted is a heartless and abusive orphanage of the kind whose story has been told often in recent years.

For some readers with religious convictions, though, there will be sporadic but profoundly felt moments of recognition. Pullman’s world is not a “disenchanted” one; it is a world where matter and meaning are woven inseparably, as surely as they might be for an Eastern Christian theologian or for a Henry Vaughan or Thomas Traherne. “Nothing is just anything.” It is a perspective that is more capacious than Pullman’s polemical moments might suggest – one that opens the door to a conversation about what the spiritual means.

La Belle Sauvage: The Book of Dust, Volume One

Philip Pullman

David Fickling Books, 560pp, £20

Listen to New Statesman culture editor Tom Gatti interview Philip Pullman for The Back Half podcast on iTunes, Acast, or via the player below:

Pullman also discusses his new book at Southbank Centre's London Literature Festival on Friday October 20