Kormac was chasing him when he was captured by Dark Cultists. After the player(s) free the Templar, he asks them to help him kill Jondar. After Jondar is defeated, he tells Kormac that he was led astray by the Coven's evil magic. But Kormac, unforgiving of betrayal, kills him without mercy.
It is learned through conversations with Kormac throughout the game and his perusal of Jondar's notes that Jondar turned against the Order soon after reading the "key words" that restored his memories of life before the Order recruited him, and it's presumed that Maghda and her minions found him shortly after this and turned him to their side. Kormac also discovers plans in Jondar's notes for angelic weapons made for human hands, with runes similar to those that grace the armor of Tyrael.