Long before Aegon's dragons ever crossed the narrow sea, the Faith of the Seven had already armed itself twice over: the knightly Warrior's Sons and the foot-soldier Poor Fellows both answered to the High Septon rather than any crown, a standing force that predated the Iron Throne by centuries and owed the Conquest nothing.
King Aenys I's weak rule gave the Faith Militant its opening, and his own household gave it cause: when the king let his son and daughter wed one another in the Valyrian fashion, the High Septon denounced the marriage as abomination, and the Swords and Stars rose openly in 41 AC. Six years of scattered war followed under Aenys's successor Maegor the Cruel, and Maegor's considerable cruelty — a golden dragon bountied on every Warrior's Son's head, a silver stag on every Poor Fellow's — broke both orders as fighting forces, though not before the fighting had cost House Targaryen dearly in blood and reputation alike.
Jaehaerys I's settlement of 48 AC formally disbanded both orders: the crown's protection of the Faith, guaranteed in exchange for the Faith laying down its own swords. The bargain held for roughly two and a half centuries. It did not hold forever — a barefoot High Septon risen from the Poor Fellows' own ranks took the crown's weakness during King's Landing's hungriest season as cause to re-arm that order, and this chronicle notes, without pretending to know how the matter resolves, that a Faith the Iron Throne once broke by force may now be owed considerably more caution than the Throne once thought it needed to spend.