The Magic Flute, with its mixture of solemn ritual and nonsensical pantomime, usually takes place in an exotic Fantasyland. When Ingmar Bergman filmed the opera in 1975, he surrendered to the artifice by setting it in a theatre, with an audience of enraptured, unquestioning children. Branagh, who is writing the screenplay himself, wants his version to be tougher, harsher; he is also keen to give Mozart's story about two courting couples an epic breadth, so he set the opera in a combat zone during the First World War. The Queen of the Night, Mozart's villain, enters astride a tank, and Sarastro, the humane conscience of the story, shelters refugees in a field hospital.

In 1920 Cambridge philosopher Goldsworthy Lowes Dickinson wrote a literary epilogue to The Magic Flute which oddly anticipates Branagh's scenario. In the aftermath of the First World War, Dickinson sends the hero, Tamino, on a search for faith, during which he experiments with Christianity and Buddhism. We are now living in the New Age, so for Branagh the spiritual quest has become a matter of personal growth. As the producer Pierre-Olivier Bardet told me: 'It is a film about becoming an adult, becoming a true human.'

The journey happens against a background of machine-gun fire and mortar attacks. Branagh accordingly began his research at the war cemeteries of northern France. 'I had a ghetto blaster with the opera on it,' he told me, 'and I ran round a fi eld in circles while it played the overture, with the producer and the production designer chasing me.' Ever the actor, he illustrated his requirements with some circuits of an imaginary maze. 'We needed to measure the distance I travelled in six-and-a-half minutes, so we'd know how long to make the trench we were going to build. The answer was 150 metres!' He has staged the overture in that muddy, rat-infested warren, with Tamino leading his recruits over the top while a runner pants the length of those 150 metres to deliver an urgent communiqué to a general.

The camera - in Branagh's lovingly detailed, elaborately visualised script - surveys a cloudless sky, glides down across a peaceful landscape, tumbles into the seeping tunnels where the troops huddle, then ventures back to the surface to document a gas attack; as we watch, Tamino changes from a dandified officer modelled on Rupert Brooke to a wild, terrified casualty like Martin Sheen in Apocalypse Now. With the images precisely matched to Mozart's changing tempi and his instrumental solos, this long introductory episode will happen without a break. 'Yes,' said Branagh, 'that's how it will look. Actually, it's six separate shots, and some of it will be filled in by computer graphics. Oh God, why did I tell you that? I shouldn't give away my tricks!' But the opera is about magic, and magicians delight in telling us that we have been deceived. The art, like that of film, lies in making us believe in what we know to be an illusion. Cinematic magic these days takes the form of digital imagery, and coloured screens leave room for 50 minutes of CGI wizardry. Work in the studio ends soon - which will let Branagh present a showreel to potential distributors at the upcoming Cannes film festival - but after that months will be spent adding electronic marvels and turning blank walls into fantastical vistas before the film's release in 2007.

Magic happens in a virtual world, but the sets built on three gaping stages at Shepperton looked hyper-real. Basket weavers lined the walls of the labyrinthine trench, and experts in ordure sprayed the fresh cane with slime and positioned puddles of pigeon shit. For the hospital ward, money was spent distressing and dirtying the mattresses on the cots. They arrived pristine; a week or so later they had been stained with a stiff crust of blood and sweat. The exterior wall of Sarastro's palace had a little rivulet dribbling from its terrace, and someone had painted a furry skin of moss on the artificial rock. No wonder Branagh has engaged Liz Smith to play Papagena, the cackling crone who lusts after the terrified bird-man Papageno: among so many fresh young faces, she looks as authentically weathered as the sets.

Mike Reading, in charge of construction, guided me through the interior of Sarastro's palace. With a magician's eye of his own, he deciphered the deceptions of the craftsmen. 'They sand-blast the floor, then fill the joints with liquid cement. And look how they've given the chandeliers that silvery tinge to age them. See those friezes above the door on the second floor? The plasterers carve them in relief, even though the camera mightn't even come near them. You wouldn't get our trades on a building site! And everything's always on time: Ken begins shooting here next week, so we can't wait around for an order from B&Q.'

The looking-glass world of film has its ironies. If you hire builders to work in your house, they cobble together something that probably falls apart a few minutes after you pay them. But film sets - ephemeral structures, not meant to be lived in - are built by perfectionists who a thousand years ago would probably have been sculpting stone and tinting glass in a Gothic cathedral.

Architecture like this emerges from nothing and after a few weeks returns to that state. The palace - with its monumental staircase, its galleries, alcoves and weathered wooden beams - was created in order to be destroyed. The script explains that it has been bombed, and on my first visit it was strewn with feather-light boulders. Next time I saw it, scaffolding in the hall announced that Sarastro, after winning the war, had begun to repair his headquarters. 'A year ago this was Gotham City,' said Reading. 'They built half of New York here for Batman Begins. Then last Christmas it was just empty space, with some tape on the floor to mark where the walls of our set were going to be. And by the end of April it'll all be empty again. When Ken's finished, we pull the palace down and chuck the lot in a skip.' The set's fate touchingly matches that of music, which materialises in the air, allures us - as a chorus in The Magic Flute says - with the hope of a better world, and then evaporates into silence.

Film-making is a manic-depressive business, a bit like war. Brief spasms of action give way to hours of slumped inactivity, during which a lens is changed or the lighting reconfigured. On a battle fi eld littered with plastic barbed wire, in the shadow of a strafed Flemish windmill, I waited for the next shot: the Russian soprano Lyubov Petrova, cast as the Queen of the Night, was to perform the aria in which she incites her daughter Pamina to murder Sarastro, mouthing while the soundtrack she recorded last year was played back. I passed the time by talking to Roger Lanser, the director of photography. 'What do you call that stuff she sings?' he asked. 'Kalahari, is it? Cocolala something?' He didn't need me to tell him that it was coloratura; Lanser, being Australian, felt blokily obliged to pretend that he knew nothing about art.

I asked Lanser about the oral probe that, according to Branagh's script, was meant to complete the Queen's aria: the camera plunges into her mouth, slithers past the epiglottis and the vestibular fold, wriggles between her gristly vocal cords, then roves at liberty through her lungs, her larynx and her diaphragm, all in an effort to show how a human body convulses itself to produce this unearthly sound. 'Ah yeah,' said Lanser, 'the tonsil-tickler - the Deep Throat shot. Mate, I hate to tell you this but they've cancelled it.' Those few seconds of film would have cost £60,000.

I reconciled myself to remaining debarred from Lyubov Petrova's interior. But I had a compensatory treat. 'Lyuba's ready for her harness,' yelled an assistant, before she emerged in a truss which was a fetishist's dream, directly wired to the roof. As she contined lip-synching her tirade, she lifted off the floor and flickered through the sky like a psychotic fairy, her arms flailing. A wind machine sent a gale to buffet her, the camera craned to follow her jolting course, and her voice ricocheted between the metal walls. The tattered sails of the windmill behind her began to spin, then burst into flame like a Catherine wheel: her aria is a feat of pyrotechnics, and that, as Branagh well knows, means fireworks. The Queen's levitation is spectacular gimmickry, but it makes perfect sense. She is called Astrafiammante, or flaming star, and her coloratura shoots astral sparks through the night sky. Her music is in fact already playing in outer space. The Voyager satellites carry a recorded digest of life on Earth, for the information of any intelligent beings who might intercept them. Among 90 minutes of music, the only operatic excerpt is the Queen of the Night's aria, which, with its piercing F sharps, testifies to human accomplishment at its dizziest and most supernatural.

The Magic Flute describes a cosmic war between the irrational darkness of the Queen and the enlightened values of Sarastro. In Branagh's version, it also describes a world at war, with nations bombing and gassing each other. But the film concentrates on a family romance, laid bare by close-ups. Cinema is defined by the camera's searching proximity to the face. During the session with the Queen, Branagh told me: 'We're trying different lenses, just to see how close to her we can get as she cracks up.' Rejigging the story, he suggests in a confi dential flashback that she and her deadly foe Sarastro were once lovers; the heroine Pamina is their daughter. The intimacy of the medium miniaturises opera, scaling down its grandiose gestures. 'Please don't act,' Branagh implored his cast during rehearsals. 'Do nothing!'

For Amy Carson - cast as Pamina a few months after graduating from Cambridge - doing nothing involved not singing. She recorded her celebrated G minor aria for the soundtrack, then found when filming began that Branagh wanted her to think her way through it without moving her lips (as he did with the hero's soliloquies in his own film of Hamlet). While Pamina considers suicide, we overhear a voice that is her silent stream of consciousness. Amy shivered at the memory. Or perhaps she was still cold from having spent the morning in drenched clothes on a frigid set, being thrown about inside that revvedup windmill. 'I'd never sung opera before this,' branagh wanted to give mozart's story an epic breadth so he set the opera in a combat zone she told me. 'I really didn't know about it. Maybe that's why I wasn't nervous when I auditioned, I treated it as a bit of a laugh. Someone played me Kiri Te Kanawa's recording of my aria the other day - I'd never heard it, I don't think I'd even heard of her. Now I'm sure I don't want to go into the opera world, it's not for me.' Her sweet candour explained Branagh's choice: rather than an immaculate voice, he was searching for an ingenuous face that would allow the camera to spy on its nervous uncertainties. Later in the day I saw Amy outside the soundstage, scoffing a fry-up from a styrofoam carton dispensed by the catering wagon as she chattered to the electricians. No, I thought, this is not a nascent diva.

A newcomer can play a neophyte, but the role of Sarastro requires authority and a patina of wisdom. He is Mozart's Zoroaster, a benevolent sun to balance the Queen of the Night's lunacy; his cavernous low notes anchor the opera, and reprove her groundless, soaring coloratura.

Almost inevitably, the film-makers engaged the great German bass René Pape, who, with a grimace of reluctance, consented to relearn his part in English. 'Don't ask me about the text,' Pape commanded when we were introduced. I didn't, since I share his opinion of it: Branagh's crony Stephen Fry has supplied a new translation that consists of relentlessly arch rhyming couplets. To revenge himself, Pape interpolated the odd unidiomatic German consonant. In a scene I watched, his voice on the playback repeatedly told Tamino and Pamina 'Your time of twial has begun'.

On the dusty set, Lyubov Petrova protected her precious vocal cords by wearing a surgical mask; Pape, however, sealed himself inside a fug of nicotine fumes. I asked if cigarettes weren't bad for his voice. 'Obviously not,' he boomed, and beamed with self-satisfaction. 'They say, too, that smoking causes impotence. This also is not true in my case!' I think he meant infertility, but either way he made his point. Pape has an attitude to match his sovereign talent, and he once established his place in the world by telling an interviewer who mispronounced his surname: 'Say it like PAPA-rotti'.

I mentioned a remark by Bernard Shaw, who declared that in Sarastro's grave, sententious aria we can hear the voice of God. 'That might be true,' said Pape, deifying himself with a wicked grin. The last time I saw him in the theatre, he was playing the devil: as Méphistophéles in Gounod's Faust at the Metropolitan Opera in New York, he had a pitchfork to brandish, and was equipped with a writhing, rubbery tail that snaked out of his buttocks. Wasn't diabolism, I asked, more fun than preachy divinity? Pape treated me to an impromptu display of Hegelian dialectics. 'They are very close together! Maybe the devil lives in heaven and God is underneath - who knows? Somebody told mankind it was the other way around, that is all.' A bass can be expected to sympathise with the underworld, and with the illicit spirits who lurk there. Branagh's rewriting of the story also hints at a secret affinity between the opera's moral opponents. At the end, the vanquished Queen does not simply disappear, eclipsed by a rising sun of enlightenment as Mozart directs; she commits suicide, and Sarastro - remorseful, or perhaps incorrigibly attracted to the dark side - makes a desperate attempt to save her.

EM Forster, pondering Goldsworthy Lowes Dickinson's interpretation of the opera as an account of the world after 1918, wasn't sure that the trials by fire and water undergone by Tamino and Pamina could stand for the travails of 'the twentieth-century spirit'. 'Can Mozart bear so much?' asked Forster. Almost ninety years later, his question is even more pressing, and harder to answer. The Magic Flute has lost its solemn eminence, and its high-minded allegory has been overtaken by popular culture's fables of adolescent angst. Branagh's version is at home in this new terrain, and when the Queen climbs the sheer walls of Sarastro's palace, the script compares her to Spiderman. Branagh tactfully avoids the religious disputes that preoccupied Mozart, for fear of alienating any international markets. But he does dare to evoke modern political crises: Tamino and Pamina stop a tank by standing in front of it 'like the student in Tiananmen Square', and a note in the script announces the triumph of 'non-violent resistance'. Can love - to paraphrase Forster - really overcome the entrenched political and religious hatreds that menace us? At one point in the film, a gobbet of filthy refuse plops down on the head of Papageno. The script's comment is terse: 'Confirmation of an indifferent universe.' Modernising The Magic Flute, Branagh forces it to confront an existential absurdity that Mozart knew nothing about. Sarastro's field hospital is said to be 'like a lunatic asylum designed by Dali and Kafka'. On one of its beds I noticed an extra, cast as a wounded soldier, lying down to rest. He was legless, and had parked his detachable pins by the bedside. I wondered how he'd managed the trick. Then when he got up and reassembled himself for the next take, I saw that he was an actual double amputee. Some losses cannot be repaired, by magic or by music.

Even so, Branagh's final image - to be filled in by computer graphics - will hark back to the rational 18th century, when music symbolised harmony and promised to restore paradise. As the last chords die away, the flute twirls weightlessly in mid-air, turned to radiant gold by the sun. It may be too late for Mozart to save our hell-bent world. Even so, it's pleasing to think that, thanks to Voyager, The Magic Flute may one day entertain the angels, or convert extra-terrestrials to opera.

The Magic Flute will open in UK cinemas in 2007