- "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 broke out at the end of the reign of King Aenys Targaryen - Aegon the Conqueror's eldest son - and lasted throughout the reign of his successor and half-brother, 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 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.
The Faith Militant quickly seized and killed Septon Murmison, who had performed the marriage ceremony between Aenys's children.
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 Morrigen 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. The surviving members of the Faith Militant would also be granted amnesty for putting down their swords.
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 selves - 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
According to Elio Garcia and Linda Antonsson, co-authors of The World of Ice and Fire sourcebook (2014), George R.R. Martin remarked to them in passing that the story of "The Sons of the Dragon" - spanning the reigns of Aenys and Maegor, centered around the Faith Militant uprising - could easily sustain three full novels' worth of narrative. Martin also said, however, that he doesn't think he'd ever have time to sit down and write three new books, given how long it's taking him to finish the main novel series.
According to Fire & Blood, although Aegon I remained on good terms with the Faith, the question of incestuous marriage remained, simmering below the courtesies like poison. The six High Septons, who officiated during Aegon's reign, never spoke out against his marriage, but did not declare it to be lawful either. The humbler members of the Faith still believed it was sinful of both aspects - the incest and the polygamy.
Maegor was the one to trigger the uprising, by polygamously taking a second wife, Alys of House Harroway; it angered the Faith so much (since incest and polygamy are both considered as heavy sins), that Aenys had to strip him off his office and exile him to Pentos. Despite an already strained relationship with the Faith (due to Maegor's polygamous marriage), two years later Aenys foolishly announced the marriage of his daughter and son, Rhaena and Aegon; that deed poured oil on the flames, directly sparking the Faith Militant uprising.
Aenys was completely overwhelmed by the uprising 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 AC.
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 AC 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 AC, 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.
In 44 AC, the High Septon who initiated the uprising suddenly died - many suspect he was poisoned by Maegor's agents, though some suspect that his own brother poisoned him because Maegor was on the verge of destroying Oldtown but he would never yield the city before it was reduced to ashes. He was replaced by a new High Septon who was Maegor's puppet, but the Faith Militant refused to surrender and the fighting continued.
In 44 AC Dowager Queen Visenya died, last of the Conquest generation of Targaryens, and Maegor's greatest supporter throughout his life. He actually seemed to take her death in stride, but Aenys's widow Alyssa Velaron - who had been held prisoner on Dragonstone - used the confusion of Visenya's death to escape, along with her two youngest children, Jaehaerys and Alysanne, and Visenya's own sword Dark Sister. Aenys's middle son Viserys was being held hostage at the Red Keep, however, and when Maegor found out about Alyssa's escape he had him tortured to death and his body left to rot in the courtyard (trying to lure Alyssa back to demand a proper funeral, but she didn't take the bait). In 45 AC Maegor launched into a new major campaign, which resulted in him taking the skulls of 2,000 men of the Faith Militant as trophies.
Maegor's supporters, however, grew increasingly unsettled at such open brutality. By this point his mental state was becoming increasingly unhinged (even relative to his prior actions), because none of his wives could produce him an heir - many whispering that he could not continue the Targaryen dynasty on his own. In 47 AC he forcibly wed three women in a triple marriage ceremony (for a total of six concurrent wives). These three "Black Brides" were all the widows of men he had killed in his wars, of proven fertility because they already had children - among them his own half-niece Rhaena. Even then, his wives only bore him stillborn monsters, each of which greatly distressed him, and he descended into genuine madness. The first of these stillborn abominations was produced in 48 AC, to his second wife Alys Harroway of Harrenhal: his third wife Tyanna of Pentos convinced him that it was the product of an affair Alys had, so Maegor executed Alys, her midwives, the Grand Maester, and every member of House Harroway, exterminating it. Eventually, however, Tyanna was somehow made to confess that she had actually used poison (and possibly sorcery) to produce the stillbirths in Maegor's other wives - at which he cut out her living heart with Blackfyre, and threw it to his dogs.
At this point the realm could tolerate Maegor's behavior no longer. Later that same year in 48 AC a new army of the Faith Militant organized, and rebel lords rallied around the fugitive Prince Jaehaerys. Maegor's own Master of Ships Daemon Velaryon left to side with the rebels, at which all of the other great lords of the realm abandoned him in short order - among them even his former close supporters like the Baratheons and even the Tullys (who had fought against Prince Aegon for him not long before). When Maegor called on any remaining loyal lords to come to his aid, no armies came - even two of the Kingsguard abandoned him to join the growing rebel army as it advanced on King's Landing. It was only a matter of time until they reached the defenseless city. Maegor was found dead in the morning, sitting on the Iron Throne itself - it is generally believed that, late at night simply waiting for the hours to pass until the rebels came, Maegor looked down at the sharp spikes of the throne and - resolving never to be taken alive - opened his own wrists on the throne itself.
Maegor's reign of terror at an end, Aenys's rightful heir Jaehaerys was restored to the throne, ushering in an 80 year golden age for the Targaryen dynasty.