The resurrection at Magdalen College

Sometimes you can have too much light. For almost 60 years the big west window of the chapel of Magdalen College, Oxford, has been glazed with plain transparent leaded lights, and the lofty vaulted ceiling, the rood screen and the ancient reredos at the east end have been drenched in the cold light of the modern day. The stained glass in the other windows consequently suffered "face light" - light from the front - that obscured them, and the mood of the whole chapel was flattened.

It had not always been this way. Until the late 1930s, a magnificent monochrome stained glass window - a grisaille window - from the 17th century, based on Michelangelo's Last Judgment in the Sistine Chapel, had filled the west wall, and the light in the chapel was mellow and muted, so the ancient wood and the carved stone gleamed with a dull gleam. On entering, as one's eyes adjusted to the sombreness, there was no doubt one was in a place reserved for meditation and prayer.

But then all changed. The threat of war with Germany loomed, and the window was dismantled for safe keeping (ironically it was severely damaged in the process) and put into storage. The man responsible for the window went off to war, and was killed. And in the years of post-war austerity, perhaps that flatness, that mundane light of day, seemed grimly right for the times. Or perhaps people just forgot, or had more pressing things on their minds. Whatever the reason, the plain west window stayed the way it was.

In 1992, however, a member of the college called Stuart Lever became Master of the Worshipful Company of Glaziers and Painters of Glass and decided to mark his year in office by making a start on the restoration of the west window, using the original glass where possible and replacing it where it was not. He chose to restore a small panel above the main window. It looked fine.

There the matter might have rested. But in a place like Magdalen College, with a history stretching back more than 500 years and with alumni who include Tyndale, Gibbon, Joseph Addison, and Oscar Wilde, the present is an endless conversation with the past. In 1994 a film crew arrived at Magdalen for the location shooting for the film Shadowlands, starring Anthony Hopkins, the broadly factual account of one of the college's most famous recent fellows, the theologian and writer C S Lewis. One scene for the film was shot in the chapel, and the art director, unhappy with the baldness of the light from the west window, taped a painted impression of the Last Judgment scene over it, to approximate the way it must have looked in the past.

Anthony Smith, the president of the college and a former director of the British Film Institute, was impressed. Memories were jogged, archives consulted. With a handsome anonymous donation from an American member of the college, the project to restore the entire window was under way.

It was the latest twist in a tale of miraculous survival. During the Civil War, in their campaign against what were called "tokens of monarchy and monuments of superstition", Cromwell's troopers dragged all the coloured glass in the chapel windows down from the walls, laid it on the chapel floor and trampled back and forth across it on horseback until it was broken into small pieces.

The Last Judgment window in the west wall had been completed only a few years before, in the 1630s, the work of one Richard Greenbury. But mysteriously, Cromwell's soldiers left it alone. Perhaps the subdued shades were more acceptable to Puritans who could not abide the flashy greens and scarlets elsewhere; or perhaps the Last Judgment theme kept them at a respectful distance. Whatever the reason, the window was left intact and in situ. When it was shattered, some 60 years later, it was not religious fanaticism but the Great Storm of 1702 that did it. Ninety years after that the college authorities finally got around to repairing it, and the glass painter they chose to do the job, Francis Eginton, replaced the severe blacks and greys of the original with the warm coffee tones that survive today.

The filming of Shadowlands stirred Magdalen with the desire to restore that mellow glory. But where was the glass? One of the down-sides to having a history that goes back half a millennium is that you accumulate a lot of lumber. "We've got a farm outside Oxford full of stuff awaiting restoration, and we found some of the Last Judgment glass there," Anthony Smith recalls. "But when Peter Archer of Chapel Studio, the restorers, looked at it, he said there was a lot missing. So we turned the college upside down looking for the rest of it - we have acres of outhouses - but nothing came to light.

"Finally the college butler, Terry Newport, remembered that his predecessor had told him that his predecessor had told him that there was a lot of glass stored in wine boxes in a ventilation tunnel that runs alongside the wine cellars under the New Buildings [constructed in 1735]." When the clerk of works ventured down - he had to crawl 60 or 70 yards - sure enough, there it was. The boxes had rotted away and much of the glass was broken, but the bulk of it was there."

Peter Archer of Chapel Studio, a leading stained glass restorer, then set to work on the jigsaw puzzle, creating new pieces where there were gaps. The technique of grisaille is painting in reverse: first you coat the entire surface uniformly with brown pigment, made from ground glass and metal oxides; then, when dry, you pick it away with brushes and needles to create the image. "We had half a dozen people working on it and it took about nine months," says Peter Archer. "It was particularly difficult because the original was so finely done, exquisitely painted, and we had to replicate that quality."

Their long effort paid off: in the finished window it is impossible to tell the new parts from the old, and the work has become a collaborative effort by great craftsmen that spans four centuries; a work that has triumphed over weather, war and apathy to survive.