St John's Co-Cathedral

Two square towers, a flat wall, a small balcony and almost no decoration. Girolamo Cassar, the architect who finished the city, designed it in the 1570s as the conventual church of a military order, in a fortress city, forty years after a siege. The exterior is honest about that.

Very few buildings anywhere reverse themselves so completely at the door.

The transformation came in the 1660s, when the Calabrian painter and knight Mattia Preti offered to decorate the entire church. He painted the whole vault himself, in oil directly onto the stone, with eighteen scenes from the life of St John the Baptist, and redesigned the carved stonework of the walls beneath it so that the interior reads as a single idea rather than a ceiling laid over a room.

The floor is not marble tiling. It is around four hundred tombs, each slab inlaid in coloured marbles with a knight's arms, his skulls and skeletons and trumpets, and a Latin epitaph making his case. It is the richest marble floor in Europe, and you walk on all of it.

The side chapels belong to the eight langues, the same national divisions whose auberges stand along these streets. Each decorated its own and competed openly with the rest, which is precisely why they are so overwrought.

Off to one side is the Oratory, a plain room built for instructing novices, and on its end wall hangs The Beheading of Saint John the Baptist, painted in Malta in 1608. It is the largest canvas Caravaggio ever made and the only work he ever signed — his name written into the blood running from the Baptist's throat.

The composition is close to empty: a vast blank wall, the figures pushed down into the lower third, the executioner reaching for the knife to finish the job. There is no heroism in it. It is a killing in a prison yard, watched by a jailer pointing at the basket.

He had reached Malta as a fugitive, wanted for killing a man in Rome. The Order received him as a knight in July 1608. A violent brawl followed within months, and with it imprisonment in Fort St Angelo, an escape, and expulsion in his absence — the record calls him a foul and rotten limb. Two years later he was dead at thirty-eight. The painting has never left the room it was made for.