My grandfather, a rampant atheist, liked nothing better than savaging the priests that my devout Irish Catholic grandmother invited home in the hope of saving his soul. After laying into them about the dubious credibility of immaculate conceptions and self-replicating loaves and fishes, he'd declaim, with a flourish: “"And what the bloody hell is Genesis chapter six all about, eh?"”

For those not up to speed on the Old Testament, this part of the creation story deals with a category of creatures called “the Nephilim”, a non-human race that apparently inhabited the Earth around the time Adam and Eve got kicked out of the Garden of Eden. My grandfather would holler: "“What are these things? Little green men from outer space?”" At which point, the deflated priest would be led from the house as my grandmother crossed herself in the face of her husband's wickedness. Even in the 1950s, priests knew that aliens and the Church didn't compute. If there were extraterrestrials out there, their existence could effectively herald the death of God – cutting the ground from beneath key biblical truths, not least of which is the claim that humankind was made in God's image.

Half a century on, the Catholic Church is finally getting round to asking what it would mean for their religion if humankind were to establish the existence of intelligent aliens. The question weighs heavily on the mind of Guy Consolmagno. Sitting among his telescopes in Castel Gandolfo, the Pope's summer palace, Consolmagno is puzzling over whether or not the Catholic Church could – or should – baptise an alien. Were such creatures discovered, ought the Pope to consider ordaining an ET? And if the human race ever masters interstellar travel, should missionaries be sent into outer space ... ?

Consolmagno, a 53-year-old Jesuit brother from Detroit, is the Pope's astronomer, with the run of the Vatican's observatory here at Castel Gandolfo, in the hills outside Rome. Despite the aristocratic-sounding name and the arcane, slightly eldritch subjects he immerses himself in, Guy Consolmagno appears surprisingly Earth-bound: a self-confessed “nerd” from MIT, the Massachusetts Institute of Technology, who's into Star Trek.

It's his job to reconcile the wildest reaches of science fiction with the flint-eyed dogma of the Holy See. Right now, he's off on a mental meander about “the Jesus Seed” – a brain-warping theory which speculates that, perhaps, every planet that harbours intelligent, self-aware life may also have had a Christ walk across its methane seas, just as Jesus supposedly did here on Earth in Galilee. The salvation of the Betelguesians may have happened simultaneously with the salvation of the Earthlings.

“Is original sin something that affected all intelligent beings?” he asks. “Is there a sort of ‘cosmic' Adam predating even life on Earth? Is Jesus Christ's redemptive sacrifice sufficient for the whole universe? Would there be a parallel history of salvation on other planets?”

Consolmagno's job is to shore up the crumbling edifice of the Church against the acidic drip, drip, drip of rationality and science . “To me there is no clash between faith and science,” he says. “My religion teaches me that God created the universe, but my science teaches me how he did it. Religion doesn't become obsolete like a science text book. In 3000 years, people will still be reading the Bible, but they will not be reading the science texts of today.”

That tension between science and religion is the backdrop to his life's work, and Consolmagno has been granted a special dispensation from the Church to produce a book called Intelligent Life In The Universe? Catholic Belief And The Search For Extra-Terrestrial Life. Published by the Vatican's Catholic Truth Society, it explores an issue which could – theoretically – reduce the spires and steeples of Rome to rubble.

The Roman Catholic Church has, in the past, been obliged to rue its mistakes: the Crusades, the Inquisition, wartime acquiescence by certain clergy with Nazism. But it was the scientific cock-ups, not the moral ones, that really threatened the institution's authority. Having taken more than 350 years to admit its mistake in convicting Galileo of heresy for insisting that the Earth orbited the sun, the Church seems keen to demonstrate that it is no longer the natural haven for scientific dunces: hence, Consolmagno and his peculiar little book.

It's Consolmagno's job to finesse any looming doctrinal difficulties that the search for extraterrestrial intelligence may present for His Holiness Pope Benedict XVI. For instance, if aliens were discovered, then why would the Bible – supposedly the word of God – contain no information about his non-Earthly creations? If they turn out to be green blobs or sentient gaseous spirals, what's all that talk in the Bible of humankind being created in God's image? What if the aliens wanted to convert us to their God? And do ETs go to heaven? Consolmagno's role is to scientifically, metaphysically and theologically take the lethal sting out of such a debate; to marry Christian faith with the possibility of discovering a talking crab in the next galaxy.

But how does the prospect affect other faiths? According to Dr Mona Siddiqui, senior lecturer in Islamic Studies at Glasgow University, the discovery of aliens would merely signal that the human race had learned a fraction more about the universe. “The question wouldn't be: ‘What does this say about our relationship to God?', but: ‘What does it say about us in the cosmos?'.

“God would remain, but the way we think about his ‘creation' – the universe and everything in it – would change.” Unless humankind finds a way to communicate with the creator, says Siddiqui, “then the mystery of God remains”, no matter what discoveries we make about intelligent life elsewhere in the void.

Ephraim Borowski, former head of philosophy at Glasgow University and current director of the Scottish Council of Jewish Communities, also remains sanguine. “My gut tells me that the discovery of alien life would have no more impact on faith than the discovery of Australia,” he says. “When that land was discovered and people of different racial characteristics were found, there was no problem in recognising them as human. If an ET was discovered, would it be that much different?

“Even if we take Genesis literally – with the story of the creation of the sun, moon and stars – we are not told what was going on on those planets.” Although Judaism sees humans as the only creature gifted a soul, Borowski has a fanciful explanation for how humanity could reconcile something physically vastly different from ourselves – a giant self-aware spider with a gift for pottery, say – with evidence that the alien creature was just as capable of love, fear, jealousy and abstract thought as us.

“If we came across an alien with whom we could enjoy a visit to the National Gallery,” he muses, “then we might take the view that this creature was a different shape to a human and so not biologically like us, but it functioned like us – or even better than us – and so could be seen to have a soul; to be effectively human.”

Only the Church of Scientology waxes enthusiastic about the prospect of extra-terrestrial life. The Free Presbyterian Church of Scotland refused to participate in a debate related to a Sabbath Day newspaper , and the Church of Scotland was reticent in putting forward a spokesperson on the subject.

Dr Richard Holloway – the controversial former primus of the Scottish Episcopal Church – insists that only a faith which has embraced modernity could cope with the daisy-cutter level fire and brimstone that would rain down on organised religion in the event of a flying saucer landing on the Esplanade outside Edinburgh Castle. “Christianity has dealt with dinosaurs, Darwin and the emancipation of women,” Holloway says. “It gulped momentarily and moved on. Good religion is not hermetically sealed. A religion that is held with lightness and less intensity can adapt. It won't be stuck in time, but move with the times.” Ultimately, he believes, the discovery of aliens would just underscore how big a mystery the universe and its creation – or creator – remain to us mortals who are just passing by.

The central question posed by the discovery of aliens would be: “Are they fallen like us?” If so, says Holloway, did they have their own version of Adam and Eve? Did they have a saviour? If they aren't fallen, then are they living in some pre-Edenic paradise with no need of a saviour? “The biggest fact that plays against the belief in a benign creator,” says Holloway, “is meaningless pain and suffering. If we discovered intelligent life on a planet that believed in no God and was just as brutal as our own planet, then that might be seen by some as the ultimate definition of a Godless universe.”

For the Vatican and Consolmagno, the theological puzzle is more tricky. As a scientist, Consolmagno can't reject the possibility of alien life. But as a theologian he has to perform an intellectual somersault in order to make sure that the chance of an ET cropping up somewhere in the universe doesn't shunt the Christian God to the outer fringes.

Consolmagno says he believes in ETs – and that they too are God's creatures and no challenge to Rome's authority. His belief is a bit like his faith: he can't prove it, but he's certain nonetheless. “I can't be sure I'm right,” he says, “indeed I could well be wrong, but still, I have a hunch that sooner or later, the human race will discover that there are other intelligent creatures out there in the universe.”

At the core of Consolmagno's reconciliation between science and religion is an almost hippy way of thinking about spirituality and the universe. He cites the opening lines of John, Chapter One: “In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through him and without him was not anything.” He interprets this as meaning that the word of God – the spirit of the essence, the meaning of God – existed before anything else, and is part of everything in the natural universe: even a giant mindworm on a planet orbiting Alpha Centauri.

“After all, we are all made of stars,” Consolmagno says, quoting the US singer, Moby. His thinking is this: just as the word of God echoes from “the beginning” until now, in all of us, so the stuff that formed the first stars remains present within the minerals from which we are all made. In Consolmagno's worldview, God and science are one. Apart from certainty in God the creator and Christ the saviour, he believes almost everything else is unknowable. It means Consolmagno can maintain his faith in God, but still believe in the Big Bang. The Lord is an infinite physicist – an all-knowing Stephen Hawking – who started the whole process of life, the universe and everything else by flicking a switch, triggering an almighty explosion some 10 billion-plus years ago and allowing his creation to unfold in accordance with his omniscient, and highly mathematical, plan.

Consolmagno considers himself a free thinker, who wears both a dog collar and his MIT graduation ring as evidence that he can be a “fanatic and a nerd at the same time”. He's happy to point out Biblical disparities – including the bit of Genesis about the Nephilim that vexed my grand father – and say it's just silly fiction. Nor does the Bible's failure to mention dinosaurs mean that Christians have to question the existence of T-Rex. “The Bible doesn't tell you how to programme your VCR either, but you know it's there,” he adds.

Consolmagno's natural audience, he says, is the devout. “They are the people who fear even thinking about science, as it might make them question their faith. But a faith that is afraid of the truth has no faith.” Part of his mission is to show the blinkered that even the most fantastical of scientific discoveries would, at least in his opinion, not trash the teachings of Christ and the prophets. “The discovery of extraterrestrial life will not destroy the Church,” insists Consolmagno. “What it might do is help us discard the bad ideas in religion – the narrow views, the hubris, the divisiveness.”

But what about the deep-rooted paranoia evident in so many science fiction works, that alien life, if it's out there, might one day attempt to destroy humankind? “We've seen when human cultures interact that nobody comes out superior,” Consolmagno says. What about the genocide of Native Americans when white Europeans “interacted” with their culture? “Hmmm,” he says, “it could happen, I suppose, but the important thing is that the Native American culture did survive.”

Consolmagno, it seems, remains the eternal optimist. God is great. And for him, the Church, in the face of everything that we know, is safe, secure and a source of succour for the souls of us all – no matter what planet we're on.

Intelligent Life In The Universe? (Catholic Truth Society, £1.95) is out now