The geese were licensed to ply their trade during their lifespan. On death, however, they were denied a Christian burial. The prospect of such a fate for men and women of this time was frightful. A pauper's burial was bad enough, but to be dumped without ceremony on unconsecrated ground was damnation itself. The land lay within the Bishop's park-lands, and the lease for the Cross Bones ground was eventually assigned to the churchwardens of St Saviour's parish in 1665, the year of the plague. By then, the stews had been closed by royal proclamation and Bankside's fortunes were in decline. In 1853 the graveyard was closed as it was deemed to be "completely overcharged with dead".

Cross bones became a piece of local folklore and although attempts were made to build on the land, they were always thwarted. In the meantime, this part of Southwark had become rife with cholera and criminality. Redcross Street in particular was one of "a set of courts and small streets which for number, viciousness, poverty and crowding, is unrivalled in anything I have hitherto seen in London." This was according to Charles Booth's survey. The graveyard itself became a haunt for body-snatchers, or Resurrection Men, seeking corpses for anatomy lessons at nearby Guy's Hospital. Then it was forgotten about. 

In the 1990s, the London Underground built an electricity sub-station on the grounds as part of the Jubilee Line extension. Prior to building, Museum of London archaeologists conducted a partial excavation, removing some 148 skeletons. One finding in particular attracted media attention. The Crossbones Girl, as she became known, was four foot seven and aged between 16 and 19. Before death claimed her, it was revealed that her nose and cheekbones had crumbled under the weight of flesh-eating lesions. Her legs were bowed from rickets. Lack of exposure to sunlight and over-exposure to industrial pollution had caused the bending of her bones. The Great Scourge was responsible for what had happened to her face. The disease was sufficiently advanced for researchers to conclude that the Crossbones Girl had been a child prostitute. London was the Whore Shop of the World. The age of consent for girls was 13. It was believed that sleeping with a virgin cured syphilis. More than sixty per cent of the skeletal remains found at Cross Bones belonged to infants. The girl's Christian name, incidentally, was Elizabeth. A reconstruction of her skull showed deep-set eyes and a square jaw. It was the face of a girl with strength of character.