The Faith of the Seven had never made its peace with the Valyrian custom that saw House Targaryen wed brother to sister, and for a generation after the Conquest that quarrel smoldered without catching flame. It took fire in 41 AC, when King Aenys I permitted his son Prince Aegon to marry his own sister Rhaena, and worse still when Aenys's brother Maegor took a second wife, the lady Alys of House Harroway, while his first wife yet lived. The High Septon thundered against the crown, and the two militant orders of the Faith rose in wrath: the Warrior's Sons, an order of knights sworn to poverty and the defence of the Faith, and the Poor Fellows, a great ragged host of common men who called themselves the Stars and the Swords. Aenys, ever a weak and vacillating king, could not master the rising, and he died in 42 AC with the realm in open revolt.
Where his brother had faltered, Maegor answered with fire and steel. Returning from exile to seize the throne, he burned the Sept of Remembrance atop Rhaenys's Hill with the flames of Balerion and put its Warrior's Sons to the sword, offered gold for the heads of the Poor Fellows so that thousands of scalps were brought to King's Landing, and hunted the orders across the length of the realm. The Faith Militant fought on through his whole cruel reign, and Maegor's own tyrannies, the deaths of wives and rivals and the slaughter at the Trial of Seven, cost him the love of lords and smallfolk alike. In 48 AC he was found dead upon the Iron Throne, whether by his own hand or another's no man could say.
It fell to his nephew Jaehaerys I to end the long strife by wisdom rather than by fire. Coming young to the throne, Jaehaerys offered the Faith a lasting peace: the crown would defend the Seven and the septs, and in return the High Septon would disband the two militant orders and command the faithful to lay down their swords. A general pardon was granted to those who would abandon the fight. So the Warrior's Sons and the Poor Fellows were dissolved, and though ragged bands would linger in the wild for years, the Faith Militant as a power in the realm was broken. Not until the reign of the Baratheons, near three centuries later, would the Faith take up the sword again.