Unfinished? Of course. When was a cathedral ever truly finished? But in Bury St. Edmunds, Suffolk, they are getting close to it. They have been building their cathedral in fits and starts since the late 1950s, having been thinking about it since 1914. It was then that the Church of England decided to make Suffolk into a diocese and gave it a cathedral on the cheap by uprating a parish church. But now, after all this time, an extraordinary moment has arrived.

The protective sheeting has been removed. The 25 miles of scaffolding poles are being dismantled. Emerging into the East Anglian sunlight is the cathedral's brand-new 150-foot tower. It is Gothic. Perpendicular Gothic, to be precise, a style that was pretty radical in the 14th century. It is arguably even more radical now. For rather different reasons.

Carved stone has been laid upon carved stone, to precise tolerances. Flints have been knapped. Men have mixed lime mortar, not cement, to join them. Concrete has been poured - as the Romans did - but not reinforced concrete, and it is no more visible than the bricks that form the cores of the four-feet-thick walls. Carpenters have done solid work in oak. This tower, plus a new north transept, extended cloister and two new chapels, are designed to last 1,000 years. They have cost £12 million ($23m). They just don't do buildings like this any more. But the cathedral's Dean, James Atwell, could and did, with enormous tenacity. This considerable theologian was the driving force behind the commission.

This all stirs some interesting emotions. Were this a 19th or even a mid-twentieth century project, St. Edmundsbury Cathedral, as it is called after its diocese, would be an ecclesiastical and architectural footnote. It is relatively small for a cathedral, it is an expansion of an existing parish church rather than being entirely new, it is on nothing like the scale of the Gothic masterpiece of Liverpool's Anglican Cathedral by Sir Giles Gilbert Scott, which took from 1903 to 1980 to build. It is smaller than Guildford Cathedral, the under-rated exercise in pared-down Gothic built by Sir Edward Maufe between 1932 and 1966. And yet St. Edmundsbury has an undeniable power. Because it is the last of its kind, and last things resonate. It is hard to imagine the Church of England, its congregations dwindling, ever embarking on such a project again.

Hard but not quite impossible: when you visit the place, and realise that this is just the latest manifestation of a religious site going back to an Anglo-Saxon monastery in the year 630, you wouldn't bet against future developments. The freestanding belltower alongside the cathedral is Norman, a surviving part of a large later Benedictine abbey. Its ruins sprawl out behind the new cathedral. This long evolution explains the appearance of the new tower. You could argue for something in glass or titanium - this is part-funded by the Millennium Commission, after all, which bought into a lot of that kind of stuff - but it is an argument you would lose. Rising above the roofscape of this ancient town, the new tower is all about permanence and continuity.

Inevitably this is not the first design for a tower. The architect for the cathedral from the 1940s until his death in 1994 was Stephen Dykes Bower, one of a small handful of architects to carry the flame of the 19th century Gothic Revival as if modernism had never happened. The porch, the first part of the cloister and entire east end of the cathedral are his. You'd never know it, but they date from the 1960s and 1970s. He envisaged a tower capped with a spire rising to 200 feet. He even left £2m in his will to help it on its way. But he designed it in somewhat Continental fashion as a kind of sweeping pylon - not unlike the spike on the Empire State Building, though in traditional materials. In ultra-conservative Suffolk, it was deemed to be un-English, a bit too showy. So Hugh Mathew - Dykes Bower's assistant - and Pethers went back to the first principles of Perpendicular Gothic to design a shorter, more familiar, but costlier, tower. Why do traditional church designers have names out of 19th century novels? Warwick Pethers, as it happens, is a youngish designer, but trained under Dykes Bower in the last years of his life, so the tradition continues.

"A strong argument for this kind of architecture today is bio-diversity," says Pethers. "We should never let anything die out completely. You never know when you might need it again." Inevitably there were those calling for a modernist tower but on the whole, says Pethers, he has encountered less hostility than his late boss, who was simply not understood by the ruling architectural establishment.

"One of the reasons we've got away with this is that modernism is now discovering its own history," he says. "There's more of an open-heartedness than there used to be. Architects of other persuasions tend to say, 'good for you'. We've had it easier than Dykes Bower. He was despised in the 1950s and 1960s."

Nonetheless, there has been more than a modicum of friction between the cathedral officials and their single-minded designer. There was a struggle at first to prevent the tower design being handed over to a larger firm of architects. Things have not been all sweetness and light since. Regrettably, it seems that people have been taking sides in what could be construed as a power struggle. Nerves are strained, tensions have run high. My sudden arrival at the new cathedral caught everyone on the hop, and at first they tried to discourage photography. Supporters from both sides subsequently contacted me, in the nicest possible way of course, to try to establish what line I was going to take. There are those who hate Pethers, with undisguised venom, and those who admire him greatly. The world of traditional and ecclesiastical architecture, it seemed, was all a-twitter. I felt as if I had walked into a real-life version of William Golding's great doom-laden novel of over-ambitious cathedral-building, "The Spire".

Well, set all that to one side. And set aside any preconceptions or dogmas about what architecture in the 21st century should be. The type of architecture - ancient or modern - is irrelevant, so long as it is heartfelt. Cedric Price, the late great British architectural theorist, once vouchsafed the opinion that the style known as high tech was in truth little more than "industrial chic". For true high-tech, he suggested, look at the assemblage of blocks of stone in medieval cathedrals, with their millimetre-thin joints. No lasers or computer-controlled cutting techniques for them. The achievement was prodigious

At St. Edmundsbury Cathedral, the quality of the end product is not in doubt, even if today's craftsmen are perhaps no match for their high-tech master-mason forbears. The design is not just about a Gothic treatment of the tower (which will act as a giant lantern, bringing daylight directly down to the altar placed at the centre of the crossing). The tower is accomplished, but externally does not have much by way of mystic power. For me the most successful part is inside, in the north transept gallery originally designed by Dykes Bower and now completed by his successors. Almost like a chapel in itself, this austere space - no applied colours, clear glass windows - sits half-concealed behind stone columns. From there your view of the altar is an unusual end-on one, from high up.

Pethers regards Gothic as "a Pan-European language that is spoken in a local accent". Hence the East Anglian references in the tower, such as the panels of flint. Inside, however, he plays a different game. "Dykes Bower's concept was to make a place that looks bigger and more mysterious by having spaces beyond spaces - to create spatial ambiguity at the limits of the building," he says. The north transept gallery does just this. It is slightly removed, certainly mysterious, incredibly subtle. The very opposite of one-liner architecture.

And so the last of the Anglican cathedrals edges towards its completion in the summer. We shall not see its like again. The Gothic Design Practice is mostly kept busy on restoration work from the last Gothic revival, when swathes of Victorian churches were built in the expanding cities. It is competing to design other, smaller, new churches. But - wouldn't you know it - even now, St. Edmundsbury still has a bit missing. The cloister has still only got two sides. A corner needs to be filled in to complete the picture, and Pethers has designed it. The cathedral's car park is in the way, so no joy yet. Of course it should be built. He may have to wait a while for the air to clear and the public response to the new works to be gauged. But in the Trollopian world of the Church, nobody rushes into anything. Everyone is used to that.