Don't tell Dan Brown ...

It has taken nearly 250 years for Nicholas Hawksmoor to emerge from the shadows of his more famous collaborators, Christopher Wren and John Vanbrugh, and despite his ascent up the league of great British architects, there is still something of the night about him. Hawksmoor's churches, in particular, have always seemed better suited to funerals than weddings. In modern times, he has become a poster boy for occultists, studious goths and historical conspiracy theorists - he has even been labelled "the devil's architect".

Through efforts of the imagination as much as through research, Hawksmoor's work has been woven into a parallel history of London's underworld, particularly his Christ Church Spitalfields, near which Jack the Ripper performed his grisly murders in the 1880s. Published in 1975, Iain Sinclair's feverish poem Lud Heat suggests that the sites of Hawksmoor's London churches form an invisible geometry of power lines in the city, corresponding to an Egyptian hieroglyph. Peter Ackroyd built on this myth a decade later with his murder thriller Hawksmoor; and more recently, graphic novelist Alan Moore threw his pointy hat into the ring with the encyclopaedic From Hell, in which Hawksmoor, the Ripper, freemasonry and the monarchy were conflated into a grand Victorian conspiracy.

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To be fair, Christ Church Spitalfields does fit the bill of a temple of dark forces rather magnificently, particularly before its recent clean-up, when layers of black soot accentuated its looming spire and dark recesses like stage make-up. His freemasonry, his fondness for "pagan" symbols such as pyramids and obelisks, and the lack of solid biographical detail have made Hawksmoor the ideal candidate for an 18th-century man of mystery. It's a good job Dan Brown hasn't cottoned on to him yet.

But by the 1950s, many of his key works were in a precarious state. Christ Church was close to being demolished, before the Hawksmoor Committee was founded to save it. The restoration job took longer than the original construction, but a gleaming Christ Church reopened in 2004, and is up for this year's Riba conservation award. Similarly, St Luke's Old Street (by Hawksmoor and John James) was restored in the nick of time, reopening three years ago as a rehearsal space for the London Symphony Orchestra. Now, the restoration of another threatened Hawksmoor church, St George's Bloomsbury, has been completed, and another veil lifted from Hawksmoor's shady character.

Like Christ Church, St George's Bloomsbury was one of the "fifty new churches" commissioned in the second wave of church building, for which Hawksmoor was one of the chief surveyors, after the Great Fire of London. In the end, only 12 churches were built, but Hawksmoor designed six of them and co-designed another two - and they are arguably the crowning achievement of his career. For many architects today, they represent the finest and purest buildings any English architect has ever produced.

St George's Bloomsbury was more of a challenge than most for Hawksmoor, although it doesn't look it. Perhaps it is secretly part of a giant Masonic hieroglyph, but the church was positioned here, on Bloomsbury Way, to cater both to the posh folks to the north, and the crime-ridden area known as The Rookery to the south. (As an indication of the area's social standing, you can see the church's unmistakable spire in the background of Hogarth's Gin Lane.)

Unlike Christ Church, the Bloomsbury church had to be sandwiched into an existing street. The allotted site posed considerable problems, since it was longer running north-south than east-west. Ideally, in Christian tradition, the altar would be at the eastern end of the church, but in this case, that would have made for a short, wide nave rather than a long, narrow one. A sort of limited competition, between James Gibbs, Vanbrugh and Hawksmoor, was held to see who could come up with the best solution. The commissioners chose Vanbrugh's design, which put the altar to the north. But Hawksmoor persisted, and eventually won through, with an ingenious plan that allowed for an east-west orientation.

The nave of the church appears to be a perfect cube, with the altar in an apse to the east. The grand six-pillared portico to the south, facing the street, was largely ornamental, and the real entrance was beneath the tower to the west, at the "back" of the nave. But the interior is actually asymmetrical, with an extra strip of space beyond the pillars at the northern end of the cube, screened off and used as a private space for the rector.

Within a year of the church's opening in 1731, however, there were complaints about the lack of space. By 1781, the entire church had been re-oriented to the north to make more room. The pews were shifted round 90 degrees, the huge wooden reredos (the wooden screen behind the altar) was moved to the north wall, and the windows behind it were blanked out. And that is more or less how the building stayed.

The church has seen its share of history - the baptism of Anthony Trollope, the funeral of suffragette Emily Davison, a requiem attended by Haile Selassie - but, despite its position on the tourist trail between the British Museum and Covent Garden, the surrounding area's fortunes have not improved all that much since Gin Lane. Ten years ago, the church's southern portico was a sanctuary for drug-users. Perry Butler, the current rector, remembers having to don rubber gloves and clear up the used syringes. His congregation had shrunk to 20. Water was seeping in through the roof, plaster was falling from the portico, and the building was put on English Heritage's Buildings at Risk register. With the help of the World Monuments Fund, the Heritage Lottery Fund, and the late American benefactor Paul Mellon (described in a plaque in the church as a "galloping anglophile"), a £9.2m restoration began in 2002, directed Colin Kerr of Molyneux Kerr Architects. "When I asked for a brief," says Kerr, "they said, 'make it flash'."

He interpreted that as a licence to bring the building back as close as possible to its original state. The east-west layout has been reinstated, and the blanked-out windows are glass again. A new stone floor has been laid. But it was more a process of subtraction - taking away messy additions, replacing stained glass with clear, stripping away the gaudy 1970s paint job, and bringing back the original stone-coloured distemper.

Like Christ Church Spitalfields, St George's will host music events, and the crypt has been transformed. Formerly a corridor with walled-up chambers of bodies either side, it is now an open space that will house an unspecified long-term tenant and a permanent exhibition on Hawksmoor and Bloomsbury.

Then there's the tower. This is surely the oddest church tower in the land: a pyramid, of all things, topped by a statue of George I in Roman garb, with pairs of lions and unicorns cavorting around its base. These lively beasts are a new addition by sculptor Tim Crawley, based on what evidence remained of the originals, which were re-carved into baroque knots in the 19th century. Hawksmoor modelled the pyramid itself on descriptions of the Mausoleum at Halicarnassus, one of the seven wonders of the world. For some, this representation of a pagan temple on top of a Christian church is exhibit A in the case for Hawksmoor as "devil's architect", but Kerr thinks the explanation is more innocent: "He'd been fascinated by the mausoleum since he was a young architect working in Wren's office. When the church was started, George I was on the throne, but by the time it was completed he was dead. So I think of this as the apotheosis of George I, with these great beasts as his protectors."

Hawksmoor, like Wren, was a freemason, but in the 18th century the term didn't suggest estate agents with rolled-up trouser legs - more a devotion to religious construction. And where Wren was a scientist until he was in his 30s, and Vanbrugh had formerly been a soldier and a playwright, Hawksmoor was one of the country's first life-long professional architects.

He was passionate about all forms of religious architecture, from ancient Egypt, to Greece and Rome, to Islamic mosques and the English Gothic tradition. The cube form of St George's Bloomsbury is an allusion to the temple of Solomon in Jerusalem - the original temple and the key work for freemasons. The obelisks and pyramids scattered through his work might indeed form some elaborate "Hawksmoor code" revealing the location of the Holy Grail; or they could simply be architectural quotations from a tirelessly inventive artist.

It would be a shame to dispel all the mysteries that surround Hawksmoor. Whether or not they misrepresent the architect, they have sustained our interest in him. But, as with Christ Church Spitalfields, the restored St George's Bloomsbury is almost entirely free of funereal gloom. The interior is gloriously light and airy, and the outside, exfoliated of a few centuries of grime, is bright and clean. It still holds the shadows in places, and will doubtless look more sinister on drizzly winter nights than it does in sunshine; but it's now more difficult to imagine strange rites taking place in Hawksmoor's churches, and easier to picture scenes of everyday worship.