What exactly did Christ and the Apostles eat at the Last Supper as portrayed by Leonardo Da Vinci? For years, art lovers and tourists who have gone to visit Leonardo's great masterpiece on the refectory wall of the 15th century church of Santa Maria delle Grazie in Milan would have been hard pushed to describe the menu or even the place settings.

In truth, the great fresco had become almost too fuzzy to see the table layout clearly. A progressive deterioration over the last five centuries, due to a combination of high humidity, kitchen grease, ill-conceived restorations, rowdy Napoleonic soldiers, second World War bombs and modern urban smog had left the Last Supper dirty and dull, with its survival permanently in peril.

Thanks to a 21-year, £2.8 million restoration process, however, the Last Supper can now be moved out of the endangered species category. Those lucky enough to see the newlook work (on view to the public from yesterday) will be confronted with sharper, brighter and fuller colours which, depending on your viewpoint, either restore Leonardo's work to its original glory or betray the great maestro's creative intentions.

As for the supper itself, all is now revealed from behind centuries-old layers of dust and dirt. Leonardo's Christ and Apostles ate a meal based on fish, oranges and lemons. They had two dishes in front of them, one for food and the other for washing their hands, while the fish was laid out on a central plate. The place settings comprised wine glasses and knives, but no forks.

Pinin Brambilla Barcilon is the woman who has had the onerous task of overseeing the restoration of the Last Supper. She has spent much of the last 21 years locked into what she describes as a "silent conversation between restorer and author". Her task has been doubly difficult. Not only was the masterpiece in poor condition when she began but also the very process of restoration was inevitably bound to attract hostile criticism.

The earliest documentary evidence suggests that the Last Supper has always been a sickly painting, already under attack from mould generated by the refectory's damp wall even before Leonardo had finished. Painted between 1494 and 1498 on commission from Milanese noble Ludovico il Moro, the Last Supper prompted initial exasperation from the Dominican prior of the day at Santa Maria delle Grazie. He complained that Leonardo was working too slowly, fearing he would never get the work finished. By way of reply, Leonardo threatened to model the figure of Judas on the prior. (In truth, Leonardo did not carry out the threat).

Pinin Brambilla confirms that the painting has had problems, almost from day one, adding some substance to the prior's complaints when she says that the source of the initial problems is to be found in Leonardo's "slow" methods: "Many people insist on calling this work an affresco but that's not right. The affresco is a technique that requires you to work very quickly, whilst Leonardo was a slow, reflective painter. For that reason, he chose to work `a secco' (on dry plaster), dealing with the refectory wall as if it were a huge tempera."

In layman's terms, this means that Leonardo did not paint the Last Supper on to wet plaster in the established fresco tradition but rather painted on to dry plaster using "tempera grassa", a sort of pigment containing oil, eggs and other binding substances. The painting, rather than sinking into the fresh plaster, remained more on the surface of the dry plaster, thus making the work extremely fragile.

Leonardo may be at fault not only for his choice of technique but also for his choice of wall, since he opted to paint on the dampest wall in the refectory. Pinin Brambilla says that the humidity level in the refectory was so bad that the wall on which the Last Supper is painted could best be compared to the inside of a bathroom window on a winter day. (The post-restoration refectory has been fitted out with special anti-UV glass windows and an air purifier while no more than 25 people at a time will be allowed to view the work).

Within 60 years of Leonardo finishing the work, 16th century writer Giorgio Vasari was reporting that the painting was falling to bits. Grease from the nearby kitchen did nothing to help nor did the fact that Napoleonic troops stabled their horses in the refectory in 1790s, using the painting for target practice. Even the second World War left its mark, since Allied bombs half-destroyed the refectory in August 1943. Miraculously, the Last Supper wall was left standing but the bombing did leave it exposed to the elements.

Nor did a number of restoration attempts in the 18th and 19th centuries improve the situation. For example, in 1821 restorer Stefano Barezzi tried to dismantle the painting, taking it down in pieces. Fortunately, he failed but not before he had done considerable damage, damage he repaired with coloured wax.

By the time, Pinin Brambilla and her team came to start work in 1978, they found that 17.5 per cent of the 45 square metre masterpiece was missing. Their work since then has consisted in both cleaning and filling in the masterpiece. Tiny squares of Japanese paper dipped in various solvents were used for the cleaning, while the "filling in" was done by painting water colours on to white plaster, a current restoration technique that has the advantage of being easily reversible.

The end product sees a Last Supper resplendent with new blues, reds and even white in which, for example, the apostle Matthew has been transformed from middle-aged and brown-haired to young and curly blonde. Inevitably, too, such changes do not meet with universal approval.

Prof James Beck of Columbia University, a man who was critical of the Vatican's restoration of Michelangelo's frescoes on the Sistine Chapel ceiling, has said that this restoration is "more Brambilla than Leonardo". The restorer, for her part, refuses to be drawn into a public squabble, merely commenting that "every restoration produces controversy". Prof Beck and others like him may have good reason for their misgivings. However, it is unlikely that the restoration process would much upset Leonardo, a man who was nothing if not a devotee of scientific innovation and experimentation.