- "When Aegon's heir wed his daughter to his son, the Faith could brook such abomination no longer. The High Septon led the denunciation of the Targaryens, and all over Westeros the Faith Militant took up its swords against the dynasty and its supporters."
- ―The High Sparrow
The Faith Militant uprising was a major rebellion against House Targaryen by the Faith Militant, the military order of the Faith of the Seven. It lasted throughout the reign of King Maegor Targaryen.
After Aegon I Targaryen conquered and united the Seven Kingdoms (except for Dorne) in the Targaryen Conquest, the High Septon at the time - after much prayer - decided to accept his new reign, and personally anointed and crowned Aegon as Lord of the Seven Kingdoms. Yet while the Targaryens had nominally converted to the Faith of the Seven, the dominant religion in Westeros, they never wholly accepted it - specifically, the Faith's strict condemnation of incest, which it held to be an abomination. The Targaryens had incestuously married brother to sister for generations (whenever possible) to "keep the bloodline pure", in the custom of their Valyrian ancestors. For that matter, Aegon I broke not only the Faith's rules against incest, but its rules against polygamy, as he was married to both of his sisters at the same time: Queen Visenya and Queen Rhaenys.
The Faith wasn't in much position to challenge the victorious Targaryen army after the Conquest or their massive dragons, but Aegon I was wise enough to tread lightly with the Faith: both sides tacitly agreed that the Targaryens' incestuous marriages were a relic of their past, which would soon fade. Aegon I didn't intend for future generations of his new dynasty to continue to have incestuous marriages, and in return, the Faith didn't press the matter for the remainder of his life. Aegon I eventually died and was succeeded by his elder son, Aenys I Targaryen, his only child by his sister-wife Rhaenys.
To the surprise of all, however, later in his reign King Aenys tactlessly wed his daughter to his own son. The incestuous marriage of Princess Rhaena and Prince Aegon broke the Targaryens' prior promise to the Faith, which could stand the abomination no longer. The new High Septon led the denunciation of the Targaryens, and the military order of the Faith of the Seven, the Faith Militant, rose up in open revolt.
King Aenys proved to be an utter weakling in the face of the revolt and was completely overwhelmed. As the Faith Militant attacked lords that still supported him across the Seven Kingdoms, one particularly zealous force of the order even managed to scale the walls of the (still under construction) Red Keep, and would have killed Aenys and the royal family if not for the intervention of the Kingsguard. Frightened, Aenys fled King's Landing entirely and retreated to the Targaryen fortress-refuge at Dragonstone - where he soon died of cramps brought on from the stress.
Instead of his own children, Aenys was then succeeded by his younger half-brother Maegor, Aegon I's only child by Visenya. Maegor was his brother's exact opposite: a highly skilled warrior and brutal tyrant, quickly earning him the name "Maegor the Cruel".
King Maegor struck back against the Faith Militant. When he arrived in King's Landing his first act was to challenge their leaders to kill him in personal combat, if they believed his rule to be ungodly. The Faith accepted, and Ser Damon Morrigan proposed they hold a trial of seven - the more dangerous but theoretically more holy variant of a traditional trial by combat in which two teams of seven men fight each other. Many tales are told of their confrontation, Ser Damon and six of the Faith Militant against Maegor and members of his Kingsguard - but all the stories agree that at the end, out of all fourteen men only Maegor himself remained alive, proving that the throne was rightfully his.
Having survived the trial of seven, Maegor promptly mounted the great black dragon Balerion - his father's old mount that Maegor mastered for himself upon his death - and flew it to the headquarters of the city's local chapter of the Faith Militant, at the Sept of Remembrance. Maegor used Balerion to burn down the sept and all who were inside while they were in the middle of the morning prayers. Hundreds of the Faith Militant burned to death, their screams echoing through the streets.
Maegor now demanded the complete destruction of the Faith Militant, and made war upon the order wherever he found it. Yet the Faith Militant would not surrender, raising its own armies across the realm, and turning some of Maegor's own lords against him. Many battles were fought as the uprising dragged on for years, lasting throughout all of Maegor's reign.
In the end, Maegor died upon the Iron Throne itself. Maegor's cruelty died with him, however, as he was succeeded by Aenys's remaining son, who became King Jaehaerys I. The new king was an intelligent diplomat and a benevolent man, determined to restore peace to the realm. Wisely seeing the benefits of uniting the crown and Faith, Jaehaerys and his new Hand of the King reached an accord with the High Septon: as long as the Targaryens defended the Faith, the High Septon would disband the Faith Militant, and cease its condemnation of the Targaryens for their incestuous marriage practices.
These were relatively generous terms, though perhaps the High Septon had little choice but to accept compromise, as by this point the Faith Militant's remaining forces were only a shadow of their former self - their armies hammered by Maegor whenever they assembled in strength, then outlawed and hunted for years. Without its own armies to enforce its will, the Faith also officially lost the right to hold its own ecclesiastical courts for religious and moral violations. For the next three centuries until the present day, the Faith Militant remained disbanded, and the Iron Throne generally acted to champion and defend the Faith. In practice, however, under particularly corrupt kings this sometimes meant that they would merely "defend" and support the High Septon and other ruling elites of the Faith with extravagant bribes, so they would look the other way and allow the kings to do as they pleased.
In the books
In the A Song of Ice and Fire novels, the Faith Militant began after King Aenys Targaryen announced that his eldest son and daughter had incestuously wed to each other, in 42 AL. He was completely overwhelmed and fled to Dragonstone later that same year, where he died while convalescing. His half-brother Maegor then seized the throne ahead of Aenys's own children and began to strike back against the Faith Militant, at which point the war truly began. The uprisings lasting throughout all six years of Maegor's reign, ending with his death in 48 AL.
The Faith Militant's main chapters were located in the largest four of the five cities located in Westeros: King's Landing, Oldtown, Lannisport, and Gulltown, and also the large town Stoney Sept located in central Westeros. At the time of the uprising, the Faith of the Seven was still headquartered in Oldtown as it had been for thousands of years - the seat of the High Septon only moved to the Great Sept of Baelor in King's Landing after it was built nearly a century and a half later. The King's Landing chapter was burned to death in one fell swoop when Maegor returned with Balerion and destroyed the Sept of Remembrance, but the rest of the Faith Militant fought on. Most of the fighting occurred in the core territories of southern Westeros: many local lords from the Reach, the Riverlands, and the Westerlands supported the Faith Militant, though none of the Great Houses dared oppose Maegor. Conversely, no uprisings occurred in Dorne because it remained independent of the Iron Throne at the time; apparently the Faith Militant also didn't have any significant presence in the North or the Iron Islands, given that they follow their own local religions instead of the Faith of the Seven (no mention has been made of lords from these regions who perhaps followed other religions but opposed Maegor for purely political reasons).
The Faith Militant uprising was not, strictly speaking, considered a "civil war" - as it is consistently stated that the later Dance of the Dragons was the first full-scale civil war which divided Westeros in half. Instead of a civil war in which two different sides officially held different territories, this was more of an ongoing series of rebellions and insurgencies: Maegor smashed the Faith Militant's armies whenever they gathered in force against him, but new ones would always pop up elsewhere.
The opening campaigns of the conflict in 42 AL did involve several major pitched battles, in which the Faith Militant's armies were supplemented by the knights and levies of various local lords. The first large battle was in the Reach at the crossing of the Mander River known as Stonebridge: some 9,000 men of the Faith Militant were caught totally out of formation as they were crossing the river, and they were slaughtered - the river ran red with blood for so many leagues that the locations was forever after known as "Bitterbridge". An even bigger Faith Militant army of 20,000 men advanced farther east towards King's Landing, but clashed with the main Targaryen army commanded by Maegor himself at the Great Fork of the Blackwater River, only a short distance west of King's Landing itself where the Blackwater joins with its tributary from Gods Eye lake. Maegor's army was of similar size but he had more heavy horse and longbowmen - not to mention, he rode the dragon Balerion into battle. The Faith Militant chose to join battle during a rainstorm, in the hope this would lessen the threat of Balerion's flames - this was true to a degree, but so great was Balerion's power that he still managed to deal considerable devastation. Maegor and his army ultimately triumphed, though not without significant losses.
The uprising continued in similar though usually smaller scale flashpoints for the next six years: Maegor would always succeed in destroying the Faith Militant's armies when they marched openly against him, but he would still end up losing men and resources to attrition, and before long more new converts to the Faith Militant would pop up again in another part of the realm far away from where his main armies had currently moved.
In 43 AL, Aenys's son and heir Prince Aegon (who had managed to avoid capture), led his own revolt against Maegor to claim the throne that was rightfully his. This was not technically considered to be part of the Faith Militant uprising, however, because the Faith was also particularly upset about Aegon's incestuous marriage to his own sister. Prince Aegon was the new rider of his father's dragon, Quicksilver, by this time over 30 years old and a full-grown adult beast. Rebel lords rallied around Prince Aegon and his dragon, and they clashed with Maegor and his army in the great Battle Beneath the Gods Eye. Prince Aegon rode Quicksilver into battle against Maegor riding Balerion - the first time two dragons had fought each other since before the Doom of Valyria. Quicksilver, however, had no hope of defeating the older and larger Balerion, then at the height of his power and majesty: both Prince Aegon and his dragon died in the battle.