THE ARTS: When Frank Cottrell Boyce wrote a film about a group of Auschwitz prisoners putting God on trial, he didn't expect to have his own faith shaken to the core by the key religious texts

PEOPLE START TO write because they think they can change the world for the better. In the end, you find that it's hard enough to make your writing better. Occasionally, though, you can change something, even if it's only yourself. You probably already know this story: a group of prisoners in Auschwitz convened a rabbinical court, put God on trial - and found him guilty. I'm pretty sure now that it's an apocryphal tale, one of those stories that persists because it strikes a chord.

It certainly struck a chord with a producer called Mark Redhead, who had been trying to turn the story into a film for almost 20 years by the time he called me in 2005 to write the screenplay.

Three years on, the result, called God On Trial, airs on BBC2 tonight. As courtroom dramas go, the story has its drawbacks: the accused is not going to break down under cross-examination, or confess all in tears. On the other hand, as Redhead pointed out, both the World Trade Center attacks and the December 24th, 2004 tsunami had seemed - in their different ways - to put God back on the world stage and raise again old questions about justice and suffering. The timing was right, but I wasn't sure about his choice of writer. Nearly any other screenwriter would have been only too happy to Dawkins up some diatribe about the badness of God. But as a Catholic, I'm actually quite fond of him and felt uncomfortable about acting for the prosecution.

Two academic rabbis, Dan Cohn-Sherbok and Jonathan Romaine, changed my mind. They introduced me to a long Jewish tradition of wrangling with God, going right back to Abraham bargaining with him over the destruction of Sodom, and forward to Elie Weisel's famous declaration that God was hanged on the gallows in Auschwitz. Here were people talking to God on a frequency that wasn't on my dial. The trial of God would not have been some blasphemous aberration, but something in the tradition of the psalms, the Book of Job and even Christ's terrible accusing cry from the cross: "Why have you forsaken me?"

Although the subject of the guilt of God is universal, when it came to writing I confined myself to imagining this particular trial: the problems of setting up a court in a blockhouse, the kind of arguments that those men might have advanced. I focused on the covenant, God's special deal with the Jewish people. I thought I was doing this to keep faith with the story - but maybe I was also doing it to distance it from my own spiritual life. The magic of stories, though, is that the more specific you are, the more universal they seem to get. The covenant turned out to be a really good way of talking about anyone who expects anything from God.

Instead of the usual snappy dialogue, I wrote speeches that ran for pages. To get them right, I had to read the scriptures: the Torah, the Talmud, everything. I assumed that doing so would enrich my own spiritual life. It almost killed it stone dead. I thought I was familiar with much of these texts, but reading them straight through was a different experience.

Here was a God who was savage and capricious, who chose favourites then dropped them, who set his people ridiculous tests. And the people! A full account of social etiquette during the time of the book of Genesis would have to include an entry under: what to do when the neighbours come around mob-handed, demanding to have sex with your visitors. The answer: offer them your virginal daughter instead.

As a writer, I was thrilled by this - free stories. Shocking, bloodthirsty stories of ancient atrocities, stories that almost everyone has forgotten. The screenwriter side of me was happy all day. But the good Catholic side of me was being beaten black and blue. I thought my faith was invulnerable. I've been through family illness. I've witnessed cruelty. I read Darwin all the time and find it feeds my faith. Richard Dawkins makes me want to pray, the same as Homer Simpson makes me want to exercise - for fear that I, too, will end up like him, a whining pub bore with the prose style of an internet conspiracy theorist.

THE FIRST REAL challenge to my faith came from reading the scriptures. It may seem deliciously ironic to you, but for me it was a time of a permanent headache and no sleep. I felt that half of me was dying.

I was anxious, too, about the Holocaust setting. George Steiner warned writers against using the Holocaust to give a story spurious extra significance and emotion. So I tried hard to keep the script as theological as possible. All the things a screenwriter is supposed to do, I did the opposite. I was vague about the setting. I tried to avoid creating interesting characters. I gave them no history except where it served the argument. When I was pitching, I said: "It's not about the Holocaust, it's about God."

Then we went to a muddy ex-military base near Glasgow and started shooting, and all that changed. The minute you saw actors - even well-fed actors with familiar faces - in those uniforms, all the intellectual theorising went straight to the background. The director, Andy de Emmony, shot the film as if it were a play, using multiple cameras and going for 10-minute takes. He was getting through 15 to 20 minutes of script a day instead of the usual four or five.

In film, the recreation of reality normally takes place in the editing suite; here, it was happening on the set, in the midst of a bunch of human beings. As the human dimension that I'd pushed to the back came to the fore, I wondered what it said about me as a dramatist that I hadn't seen this coming. Making the complex, contradictory human experience the first consideration - it's more or less a definition of drama.

So God On Trial stopped being about theological arguments, and became about the fact that people might be capable of having a theological argument on the way to the gas chamber. In Vasily Grossman's novel, Life and Fate, there is the story of a doctor who is giving someone long-term treatment for cataracts, even though she knows that both she and her patient have only days to live. Is this idiot optimism, self-deception, or a heroic refusal to submit to the dehumanising process? And where does that heroism come from? It's a fact that, although many people lost their faith in the camps, just as many had it renewed. As French philosopher François de La Rochefoucauld says: "A great storm puts out a little fire, but it feeds a strong one." Reading the Bible in the light of the Holocaust was a bit of a storm for me. It came close to putting out my fire, but in the end it blew stronger.

I didn't tell you the end of the story. After they find God guilty, one of the rabbis says: "So what do we do now?" The reply is: "Let us pray." Is this a wry story about Jewish stoicism? Is it about a failure of moral courage? Or what? For me, it's about faith.

Faith has had a bad press of late. It's been used by politicians as a rationale for going to war without reason, because it "feels right". That is not faith - that's a hunch, plus vanity. The final solution was conceived as a public-health project; its perpetrators thought it was a dirty job, but someone had to do it. No matter how extreme it was, we should remember that the rationale was completely in line with the then "best practice" in eugenics. People who are now humanist heroes - the women's rights activist Marie Stopes, for instance - were of the opinion that the gene pool needed cleaning (she stopped talking to her son when he married someone with glasses).

The camps tried to reduce individuals to components in a project. In the end, they did that literally. What good stories do is the opposite. They say the human is irreducible. Tobias Wolff has described the story of the prodigal son as "surely the most beautiful thing ever written". No one hears it without feeling the conflict between the need to do right by the eldest son, and the need to express the overwhelming love you feel for the lost one, now returned. The father is nothing without the son. That contradiction is crucial.

I'm hoping that God On Trial is a mirror image of that story. Only this time it was God who seemed to go away, and people who - inexplicably, perhaps - were prepared to rush out to welcome him back.

- Guardian service

• God On Trial is on BBC2 tonight at 9pm