The parish church of Rabat is dedicated to the Patron Saint St. Paul. It was built in 1575 and remodelled in 1692. Underneath the church you will find the grotto in which St. Paul took shelter during his months in Malta, after he was shipwrecked on his way from Creta to Rome. From there he missionized Christianity and healed sick people. Among these people was St. Publius, the father of the gouvernor during that time and one of Malta's three Patron Saints. The legend saying that scraped off stone from the walls of the grotto have healing powers are likely to base on that.
http://fullofcharacter.com/index.php/en/church-of-st-paul-and-grotto#sigProIdc9696e2be1
During roman times the grotto had a completely different use – it functioned as a prison. Holes in the sealing, used for the chains of the prisoners, are an indication to this darker history of the grotto.