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Nicholas Hawksmoor's 1729 design for Christ Church in east London is one of the finest examples of ecclesiastical baroque architecture in Europe, and one of the best instances of its creator's creed of "terror and magnificence". It has long haunted the imagination of writers and artists, who have associated it with pagan sacrifices, ritual magic, plague pits, druids, diabolical freemasonry, occult codes and Jack the Ripper – most remarkably in From Hell, Alan Moore's graphic novel and Peter Ackroyd's Hawksmoor.

Less speculatively, and more recently, the church has been the subject of a cracking detective story. It has involved tracking down ancient documents, searching for evidence in the fabric of the building itself and poring over ancient bills of quantities. The aim of the detectives is to return the church to its former glory, a process captured on the following pages by Julian Anderson (who, you may recall, did a similar job on the Millennium Bridge over the Thames a few years ago). To understand the difficulty of this task, it is first necessary to appreciate something of the building's history.

Hawksmoor's bold design enclosed the nave in a rectangular box, crowned at its west end by a broad tower topped by a steeple. The interior was just as bold, with clear-glazed windows illuminating the central nave, the two aisles and a timber gallery on the first floor. The church remained unaltered until 1822, when the interior was unsympathetically embellished with decoration and furnishings. Then, in 1866, along came Ewan Christian, architect of London's National Portrait Gallery, to finish the wrecking process. Christian's savage intervention managed to rid the church of many of its unique qualities: away went the first-floor galleries and the box pews, the windows in the aisles were blocked up and the gallery windows were lengthened. The church remained in use, but as its congregation dispersed, it began to fall into disrepair. By 1957, it had become derelict. Only the formation of the Hawksmoor Committee saved it from demolition. Under the committee's protection, the building's roof was rebuilt and its crypt was used as a rehabilitation centre for alcoholic men. The church itself, however, remained derelict.

Then, in 1976, The Friends of Christ Church Spitalfields was formed. Their mission: to restore this important building and bring it back into use. The trust set about restoring of the building's exterior, which was finished in 1999.

As work on the exterior was under way, the piecemeal restoration of the interior commenced. The trouble was that Hawksmoor had left behind no detailed drawings, so nobody knew what to reinstate – which is where the detective work started. Enter construction detective Andrew "Red" Mason, formally of architect Whitfield and Partners and now with architect Purcell Miller Tritton.

Mason scoured the interior of the church looking for evidence of Hawksmoor's original scheme. "The evidence is in the building itself – in the new stonework filling holes in the columns, in the ghost of the gallery formed from bits of varnish, paint and grease stuck to the stonework," he says. With these clues, Mason was able to suggest how the interior might have looked. But how could he be sure?

His next line of enquiry was the library at Lambeth Palace, the historic library of the Archbishops of Canterbury and the principal repository and record office for the Church of England. Here, Mason uncovered many of the original papers relating to the construction of Christ Church, including tenders from trade contractors and books of works – a kind of 18th-century bill of quantities. These books of works accurately detailed how much work each trade contractor had done each week – for example, how many square feet of plaster was installed – and how much they were paid for it.

From this information, Mason was able to deduce a full set of the components used in the construction of the church. All he had to do now was to work out where they went. Things might have been easier if the 30 drawings uncovered in the British Library had been of the final design for the church, instead of preliminary sketches. As it was, the only solution was to combine the evidence gathered from the church with that from the books of works. "You look first and then test the hypothesis against the evidence," he explains.

However, it was evidence of a different kind that brought the restoration to a halt in 1985. Eight lucky archaeologists were working on clearing more than 1000 corpses from the labyrinth of interconnecting tunnels and vaults beneath the church. At the time it was the largest excavation of human bodies ever conducted. They had to take many of the bodies from lead coffins. After prising open the lids, the archaeologists had to breathe past the stench of putrefying flesh on still-decomposing bodies, which they had to remove for analysis. It was a task made all the more disagreeable because the ventilation openings to the vaults had been sealed in case any coffins contained people who had died from bubonic plague or smallpox. These fears were realised when the body of a man, buried 140 years ago, was uncovered who had clearly died from smallpox. The Health and Safety Executive ordered the site be closed immediately and those working in the vault had to be vaccinated. The vault remained closed for six months while a laboratory in the USA analysed the corpse – before concluding that the virus was indeed dead.

After this little hiccup the restoration proceeded fairly smoothly and in 1987 the church reopened as a place of worship. By 1990, a proposal had been drawn up for the reinstatement of the galleries. Nine years later, however, and the congregation was still without its galleries and The Friends of Christ Church Spitalfields' dream of reinstating Hawksmoor's interior was still a long way from being realised.

Then, in 1999, project manager Malcolm Reading & Associates was brought on board to advise on funding applications and to manage the restoration process. Reading proposed closing the church once again for a final blitz on the interior. This would allow the specialist restoration contractors and craftsmen uninterrupted access to the interior.

Since 1999, much has been achieved, but there is still a long way to go. Restoration is expected to be completed by summer 2004, when the church will finally be returned to its former glory.