The Great Purge was a period in which Uther Pendragon enacted brutal reforms against the Old Religion, resulting in the execution of hundreds of sorcerers and the extinction or near-extinction of numerous species of magical creatures. The Purge lasted for a year, after which magic was banned from the kingdom of Camelot.
When Uther's wife, Ygraine, could not conceive an heir to the throne of Camelot, a desperate Uther struck a bargain with the sorceress Nimueh that would allow Ygraine to conceive an heir. He sent Gaius to the Isle of the Blessed to make the request on his behalf (Le Morte d'Arthur). But the bargain meant that a life had to end in order for a new life to begin, and Ygraine died in childbirth. A grief-stricken Uther blamed Nimueh and had her banished from the court (Excalibur).
The Great Purge occurred during the year following Arthur's birth. The Purge may have been foreseen by the followers of the Old Religion, as the Questing Beast an omen of great misfortune appeared the night the queen passed away. At the start of the Purge, Uther gave Gaius a list of all people suspected of using Magic to be killed; when Gaius discovered his beloved Alice on the list, he struck her name off, thus giving her time to escape (Love in the Time of Dragons). Gaius decided to stop practicing magic and to remain in Camelot as Court Physician and convert to the New Religion. During the Purge, Uther ordered many people to be drowned, including children who had inherited magic from their parents (The Tears of Uther Pendragon).
Jaden Muirden and her husband suffered this fate and were sentenced to be burned at the stake. When they were being burned, Edwin tried to save his parents but failed and was disfigured by the fire (A Remedy to Cure All Ills). Alvarr's parents were captured by Uther's forces and were burned at the stake (apparently Alvarr witnessed this happen). He was sentenced to death as well, but shortly before his execution, whether by magic or non-magical means, he escaped and fled from Camelot and later rise up against him (The Witch's Quickening). Uther, during the Great Purge, hunted almost all the Blood Guards and killed them.
Julius Borden, a pupil of Gaius, parted during the Great Purge, leaving Gaius in trouble. It is possible that The Crystal of Neahtid was kept and guarded by the High Priestesses on the Isle of the Blessed too, before it was taken by Uther and locked into the vaults of Camelot (Aithusa). The many sorcerers who died trying to protect it may have been the High Priestesses. Uther also pursued and slaughtered all Dragons except for the Great Dragon. Uther tricked one dragonlord, Balinor, to lure the Great Dragon to Camelot under the pretense of wanting to make peace with it, only to capture and imprison the dragon beneath Camelot to be an example to all who use Magic. Uther then had all the Dragonlords rounded up and killed. The Purge then ended, though Gaius helped Balinor to escape execution (The Last Dragonlord).