Infra-red photography had revealed many differences between the painting, the Adoration of the Magi, and the under-drawing. These appear “to subvert Da Vinci’s true intention”.

Amid the obsessive scholars and scheming prelates who inhabit Dan Brown’s global blockbuster, The Da Vinci Code, there is a real person.

Maurizio Seracini works in a high-ceilinged, colourfully frescoed palazzo just across the river from the Uffizi gallery in Florence. His premises are packed with machines that look as if they belong in a hospital or laboratory.

Brown calls him an “art diagnostician”, which is not a bad description for someone who probes paintings with state-of-the-art-technology, often to advise museums, dealers and collectors on their restoration.

The Da Vinci Code revolves around the contention that Leonardo Da Vinci’s paintings are full of symbolic allusions to a secret claimed to have been preserved by successors of the defunct medieval order of Knights Templar – that Christ married Mary Magdalene and had a family whose descendants are alive today. What attracted Brown to Mr Seracini was his epic investigation into what lies below the surface of the Adoration of the Magi, a work the art detective believes was sketched by Da Vinci, but painted over by someone else.
As Brown related, infra-red photography had revealed many differences between the painting and the under-drawing. These, he said, appeared “to subvert Da Vinci’s true intention”. He added: “Whatever the true nature of the under-drawing, it had yet to be made public.”

Now it can be. Mr Seracini, who could finish his four-year investigation this week, has given the Guardian an exclusive preview of the results. He provided a glimpse three years ago to the New York Times and since then, he said, he had revealed his incomplete findings to only four experts not directly involved. Mr Seracini has examined the painting minutely using a technique that exploits the fact infra-red light passes through paint but reflects off the under-drawing.

As the photographs show, he and his team have conjured from below the amber-brown layer with which much of the panel is covered a collection of Da Vinci’s drawings that were hidden for more than five centuries. They contain numerous previously invisible – or barely discernible – details. Some will electrify conspiracy theorists.

The Adoration of the Magi could have been dreamed up as a playground for semiologists. Even the visible work is packed with figures, faces, beasts, buildings, foliage and an extraordinary amount of activity, much of which bears no relation to the biblical account of the three kings’ visit to the Virgin Mary and her newborn child.

There is a ruminating figure in the foreground surrounded by a sea of faces. Behind Mary on one side, there is an oddly shaped, incomplete structure which is sometimes taken for a ruined palace. On the other side horsemen can just be made out engaged in a struggle. Missing from the scene are elements you would expect. There is no stable, no manger, no oxen, not even a donkey.

Mr Seracini’s investigation has been funded by the Swiss-based Kalpa group, a non-profit organisation that supports scholars and their research. Three assistants have worked full-time for almost a year in the final phase, enhancing and assembling 2,400 infra-red images.

Whether covered up by Da Vinci or someone else, Mr Seracini said he has found “a whole new world” under the surface which no one disputes was created by Da Vinci. There is ample documentary evidence that he was commissioned to paint an Adoration of the Magi and that he completed at least part of the work.

“You get a wonderful sense of Leonardo’s creative ferment,” said Martin Kemp, an art history professor at Oxford University and one of the few experts who has seen the partial results of Mr Seracini’s work. “The amount of brainstorming going on underneath the painting is remarkable.”

On the right, a finely depicted ox and donkey emerge from 500-odd years of invisibility along with part of the roof of the missing stable. The misanthropic king scowling over Mary’s right shoulder is revealed as a figure of composure and majesty. A host of masterfully sketched faces emerges in the lower left corner.

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Perhaps the most important discovery for critics and historians is that the two horsemen in the upper right corner are just one small part of what was originally a full-blown battle scene. The violence and horror are almost palpable: men flinch as they parry blows with their raised arms; they writhe under rearing horses. Visible through the struggle are more battling men and horses at a distance.

One question raised by Mr Seracini’s painstaking investigation is why Da Vinci wanted to include such a bloody scene in a nativity painting, and why he – or someone else – thought better of it.

But another question, and the one that will fascinate the Dan Brown fans, is what Da Vinci was up to on the other side of the painting in the last area of the panel to be fully rendered by Mr Seracini’s technicians.

The traditional interpretation is that the building is a ruin symbolising the decay of the old, pre-Christian order. Mr Seracini’s examination has confirmed the structure is not Christian. Da Vinci did not turn to the Classical Roman architecture that was all around him. “This is a lotus capital,” said Mr Seracini, pointing to the top of a column. “I was very surprised when I saw this.”

The capital, the upper portion of a column, offers one of the main clues to the age and style of a building. Capitals modelled on the lotus flower are characteristic of ancient Egypt.

Parts of the building are ruined and neglected. Another recent discovery, made just a few days ago, is that there is a tree growing out of the stonework. Yet there are people – apparently labourers and craftsmen – clambering all over it. Mr Seracini believes the building is a pagan temple, and that Leonardo originally intended to show it being rebuilt.

This is unusual in a nativity scene, but it does not take a huge leap of the imagination to see in it, as Da Vinci Code fans no doubt will, an allusion to the book’s pivotal claim: that, after the dissolution of the Knights Templar, the order was surreptitiously reconstructed so its secret could be preserved. Mr Seracini, who claims never to have read Dan Brown’s book, is reluctant to enter into such speculation.

But he is convinced that he has discovered the “true” adoration and that what we have all been looking at for centuries is a distortion created by a “very minor hand”. Sitting beside him as he summons details from the under-drawing on to a large computer screen, it is not hard to see why.

Physical details that are exquisitely rendered in the original design become deformed by the application of the top layer, which is a mixture of pine resin, shellac, carbon and bitumen.

Mr Seracini believes this upper layer was applied a half-century or more after Da Vinci. But most art historians remain unconvinced.

Some have argued the work was never intended to be seen in its current form; that the orange-brown mixture was intended merely as underpaint. Just as controversial is the question of Da Vinci’s intentions.

Mr Seracini said Da Vinci created the under-drawing as an underpainting because he used a brush and a mixture of lampblack and watery glue.

“Otherwise it would just have faded,” he added.

Was he saying that Leonardo might have suspected his work would not stay the way he intended it, and may have deliberately preserved it that way? “I’m not going to speculate on that,” Mr Seracini replied briskly. “That’s for art historians to do. But I cannot rule it out.”

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