The once-cultish literary critic Darko Suvin said that the definitional basis of science fiction was "cognitive estrangement", a hard-to-explain and almost subliminal sense that things are not as they should be.

Needless to say, most science fiction falls back instead on mere strangeness. The kind of alienation - no pun intended - Suvin was after didn't rely on names without vowels, cryptozoology or technologies that might seem advanced on the high street but already pure RadioShack in the depths of the military-industrial complex. No-one does cognitive estrangement quite as creepily well as Michel Faber, but he may be after a different game in this, his first novel for more than a decade.

It's a book that unexpectedly and briefly suffers from its perceived proximity to Faber's literary debut. There are still young men in Glasgow gasping with relief/regret at not having been unwittingly "cast" in the movie version of Under The Skin, a Scarlett Johansson vehicle in which Scarlett Johansson's vehicle carried off and then basically farmed the cream of the male population.

At first glance, The Book Of Strange New Things is more direct, plainer in plot and wears its strangeness much more prominently on its sleeve. Peter Leigh is a pastor (Faber is always concerned with the pastoral in one or other of its versions) about to embark on a long and potentially dangerous mission to an initially undisclosed location. He is set to leave behind his wife Bea, with whom he has a deeply felt and passionate relationship and who, we learn, previously rescued him from a life of drug addiction, homelessness and petty crime. So far, so Mungo Park. But this being a Michel Faber novel, we discover that Peter's destination is Oasis, a human colony somewhere in a spatial/temporal location reachable only by The Jump, a disorientating translation that has "cognitive estrangement" written all over it.

Peter survives the journey and begins to make his way in the outwardly bland normality of the settlement established by USIC (an acronym left undecoded). The setting and personnel are cleverly similar to those on the cargo ship Nostromo (Conrad reference!) which becomes the killing ground in Ridley Scott's Alien. There are a couple of nicely conventional details, like the apparent disappearance of a previous missionary. The air outside is strange and soft. The rain comes down in waves rather than drops (which might be a reference to quantum uncertainty, or it might not). The Oasan "people" - aliens? - are so butt-ugly they make ET seem as handsome as George Clooney. The Oasans exchange ambiguous foodstuffs for surplus medicines, which may or may not work for their physiology. They speak a version of English in which the sibilants and lingual stops sound like vegetation being cut and which requires a special orthography that might be Hebraic or Urdu, estranging but alarmingly easy to read after a page or two.

All of which seems fair for a conventional set-piece on aliens and alienation, but it becomes increasingly clear that the real - or at least a major - focus of Faber's attention isn't on Oasis but on what Peter has left behind. He remains in touch with Bea via the Shoot, a kind of super-email. Back "home" it is raining incessantly. There are tsunamis in the Indian Ocean, cyclones in Korea and an earthquake across the M6. We've already been warned of potential disaster in the repeated emphasis of a naive collage of the Ark in the Leighs' house. It was not created by their child, though. As yet childless, they share their living space with a resident alien, the cat Joshua, who has an initial in common with Jones in Alien as well as his biblical association. Is he "saved"? The aliens on Oasis know and love Jesus (you have to take my word about those sibilants) and about the "Book of Strange New Things", which is the Christian Bible, but yet have no distinct personality, emotions or obvious culture.

Where Faber's narrative becomes seriously interesting is its investigation of metaphor as a mode of thought. How to convey the central tropes of Judaeo-Christianity - Adam and Eve, man and woman, fishing, lost sheep, youth and age - to a "people" who do not have oceans or sheep or visible gender. And so, how to convey love and sacrifice and redemption? These are serious questions.

When I was a boy, I met the great Scottish theologian William Barclay, who took a kind interest in my then-current obsession with space travel and told me that the discovery of an extraterrestrial population with full knowledge of Christ and His love would be the greatest moment in the history of mankind. Faber understands that such a moment is thwarted not just by language but by the portals and appurtenances of the body, the functions they serve and qualities they represent.

This is not a book about bug-eyed monsters. The really scary aliens are ourselves. Though it continues the line of Faber's first book, this latest despatch is more fully the heir of The Crimson Petal And The White, his 2002 novel which was also about belief in extremis, the limits of the body and the limits of language. Together, they represent a rich triptych, an altarpiece for an age whose chief ailment is that it is not secular enough and which fatally confuses science and belief, human pursuits which rarely compete in reality and pursue quite different ends. With this, Faber eases ahead of David Mitchell and Philip Pullman (both of whom are quoted on the cover, along with in-house Yann Martel) as the apostle of our moment in and out of time.