In 1160 Henry the Lion moved a bishopric to Lübeck and planted a cathedral at the south end of the island. The merchants built their reply uphill. From 1265 the town council raised a three-aisled basilica modelled on the stone Gothic cathedrals of Reims and Flanders — but in brick, because brick was what the clay of the Baltic plain gave them.

No one had built a brick church this high and vaulted it. Buttresses take the outward thrust, and the central nave reaches 38.5 metres, still the tallest brick vault anywhere. The towers stand 124.95 and 124.75 metres to their weather vanes. Lübeck had been made a free imperial city in 1226, answerable to the emperor and nobody nearer, and the church says so out loud: it dwarfs the bishop's cathedral, and some seventy churches around the Baltic were built to follow it.

The raid on the night of 28–29 March 1942 burned roughly a fifth of the old town, taking the cathedral and St Peter's along with St Mary's. What went with the church reads as a catalogue. The Totentanzorgel, installed in 1477 and played by Dieterich Buxtehude and probably by Bach, burned. So did the monumental Danse Macabre — Bernt Notke's original had been replaced by a copy in 1701 — along with Notke's Mass of Saint Gregory, the carved figures of the rood screen, Benedikt Dreyer's saints, the medieval glass, the great organ of 1851 and the astronomical clock of the 1560s. Of eighty-four memorials standing in the twentieth century, seventeen survived.

Rebuilding ran from 1947 to 1959. The spires went back up in lightweight concrete under copper rather than timber, so a second fire could not do the same thing twice.

Some things came through. The Antwerp altarpiece of 1518, twenty-six carved and painted scenes from the life of the Virgin, happened to be stored in the Chapel of Indulgences and survived intact. The Darsow Madonna of 1420 was smashed and reassembled from hundreds of fragments, back in place by 1989. In the ambulatory a sandstone Last Supper of 1515 carries Lübeck's small joke: a mouse gnawing at a rose bush, which you touch for luck, or to guarantee you never return to the city, depending on who is telling you.

The heat also did something nobody expected. It shook loose sheets of plaster and exposed medieval wall painting beneath. Restoring it fell to Dietrich Fey, who hired a local painter, Lothar Malskat, and where no photographs existed simply had him invent the choir clerestory in fourteenth-century style. It became post-war Germany's largest art forgery scandal, and it unravelled only because Malskat turned himself in, in 1952. Both men went to prison in 1954, and Malskat found a second life as a character in Günter Grass's novel The Rat.

The astronomical clock had stood behind the high altar since the 1560s and was destroyed outright; all that survives is one dial, itself a replacement from an earlier restoration, now in St Anne's Museum. What hangs in the Danse Macabre Chapel today is one man's project. Paul Behrens, a Lübeck clockmaker, spent from 1960 to 1967 on it — raising the money, making every part himself, maintaining it until he died.

Calendar and planetary discs give the day and month, the positions of sun and moon, the twelve zodiac signs, the date of Easter and the golden number. At noon a procession of figures crosses in front of a blessing Christ. They used to be the prince-electors of the Holy Roman Empire. Since the rebuilding they are eight representatives of the peoples of the world.

One loss is still being fought over. Thomas Fredenhagen, a Lübeck merchant, paid for an eighteen-metre altarpiece of marble and porphyry carved by the Antwerp sculptor Thomas Quellinus in 1697 — reckoned by one Lübeck museum director the only work of European stature the city's Protestant church produced after the Reformation. The fire damaged it badly, the bishop wanted it gone, and after eight years of argument he won: in 1959 the chancel received a plain limestone altar and a bronze crucifix by Gerhard Marcks. Fragments stand in the ambulatory. The rest is stored above the vaults between the towers, and the question of reassembling it comes round again every generation.

The north tower now holds twelve bells, one of them a baroque instrument from a church in Danzig, now Gdańsk, hung after the war as a temporary replacement that stayed. Konrad Adenauer gave the new tenor bell in 1951, for the church's seven-hundredth anniversary. St Mary's is one of the Cross of Nails centres, the reconciliation network born in the ruins of Coventry Cathedral. Downstairs, the broken bells stay where they are.