This war and the subsequent destruction of the faith of R'hllor left the lands of Westeros fearful and untrusting of the religion, even to the present day.
The war began when King Edric I Baratheon was killed by his brother Cyral Lighthart, sometimes referred to as "The Red Stag." Cyral and Steffon Lighthart claimed to be born from Mellisandre and Stannis, and therefore felt that they succeeded Edric and even his mother, Shireen, in their claim for the Iron Throne.
With Edric dead, his only trueborn brother, Davos I Baratheon, rallied armies against the pretenders of House Lighthart. Originally only the Stormlords rallied to his cause, while the Lannisters and Florents rallied their armies under the Flame sigil. The rest of the Realm watched and waited until the Reach made a daring move to back Davos, a shift of the tide that brought many backers from the other great Houses. Their support was unnecessary, however. The Crownlands and Reach, led by the skilled and capable Davos, only needed a few victories to quell the opposing armies, and until the doom of both the Tyrells and the Baratheons, the two houses held a strong alliance.
After securing the Iron Throne, Davos declared the Faith of the Seven the official religion of Westeros. Davos’s reclamation of the faith was a bloody affair with the help of a new Warrior’s Sons, Faith Militant, and Holy Hundred, which Davos led himself. The three groups spearheaded a massive reformation. Every R’hllor-sympathizing family line Stannis had installed was overthrown and killed, and the armies of the Seven swept the land, committing genocide against the Red God’s followers. An unauthorized (but unpunished) assault on the North was made, in hopes of finally ridding the Realm of all unfaithful to the Seven. However, the invasion was predictably short, stopped immediately at the Neck. The last strongholds of R’hllor were Brightwater Keep and Dragonstone. It took a year of siege to secure the Florent’s hold, and Dragonstone claimed the lives of thousands who attempted to take it. The castle only fell after the defenders ran out of food and water.