History
The uprising was a large conflict that engulfed the Seven Kingdoms for seven years. Its root causes began in the reign of King Aenys I Targaryen. The constant (though largely unintentional) slights the Faith of the Seven suffered by Aenys led to an armed rebellion against the Iron Throne by the Faith.
The first of these slights began on the Iron Islands when a man who claimed to be King Lodos reborn was dispatched by Lord Goren Greyjoy. Goren sent the pickled head of the would-be king in a jar to Aenys, who in gratitude granted Goren a boon. Goren used it to oust the Faith from the Iron Islands to the despair of the rest of the realm and to the anger of the Faith.
The second slight happened in 39 AC when Prince Maegor Targaryen took a second wife, Alys Harroway. This marriage angered the Faith and the High Septon (whose niece Ceryse Hightower was Maegor's first wife), so Aenys tried to placate the faith by stripping Maegor of his |office and sending him into exile to Pentos. A renowned septon known as Murmison replaced Maegor as Hand of the King.
The final slight that enraged the faith and led to armed rebellion happened in 41 AC when Aenys had his daughter, Rhaena, wed to his son and heir, Aegon, receiving a denunciation from the faith as "King Abomination". Pious lords and even smallfolk who once loved Aenys turned against him. Murmison was expelled from the Faith for performing the wedding of Aegon to Rhaena and was later torn apart by smallfolk in a litter two weeks after he performed the ceremony. The uprising of the Faith Militant had begun.
Conflict
Aenys died less then a year from the conflict's start, some say due to illness caused by the strain he suffered. Many others claim he was killed by Visenya Targaryen so she could place her own son Maegor as king.
Ravens flew, declaring a new king had been crowned and that those who defied him would suffer a traitor's death. Maegor mounted Balerion, the Black Dread, and set for King's Landing to crush the uprising. Landing on Visenya's Hill he planted his standard, rallying his supporters to him. Visenya challenged those who questioned her son's right to rule to prove themselves, a challenge that the captain of the Warrior's Sons accepted.
Ser Damon Morrigen challenged Maegor to a trial of seven which Maegor accepted, with Damon and six Warrior's Sons against the king and his six champions. Maegor, the only survivor, took a blow to the head and collapsed just as the last Warrior's Son died. For twenty seven days he lay in a coma. On the twenty-eighth, Queen Alys Harroway returned from Pentos with Tyanna, whom many whispered was a sorcerer. On the thirtieth day the king awoke.
Maegor mounted Balerion and without warning flew over the Sept of Remembrance on Rhaenys's Hill, unleashing the Black Dread's flames and consuming the Sept and all within in dragonflame. Those who tried to flee were slain by archers Maegor had placed around the hill. The screams of burning and dying men were said to echo in the streets of King's Landing, and it was claimed a pall hung over the city for seven days.
At the Battle of Stonebridge, Maegor's brutal methods against the Faith made the Mander run red with blood for twenty leagues. The bridge and castle that commanded it was forever known as Bitterbridge thereafter. Another fierce battle was fought at the Great Fork of the Blackwater, a decisive victory for King Maegor whose dragon left death in its wake.
The uprising lasted all of Maegor's reign. His extremely bloody and harsh methods for crushing the rebellion gained him the name 'The Cruel'. These included placing a bounty on the heads of the members of the orders, giving a gold dragon for any scalp of a Warrior's Son and a silver stag for the scalp of a Poor Fellow. Even the death of the High Septon in 44 AC and his replacement by a more passive one did nothing to stop the determination of the Warrior's Sons and Poor Fellows.
Septon Moon and Ser Joffrey Doggett led a large army of Poor Fellows against the king in 48 AC.
Upon Maegor's death in 48 AC, King Jaehaerys I Targaryen offered an immediate amnesty on pain of the Faith Militant's disbanding, which was accepted. For this, Jaehaerys I was given the name 'The Conciliator'.