So to understand the conflict (known as the Fitna) we have to start with Uthman bin Affan the third Caliph. He was from the Umayyad clan and gave preferential treatment to his clansmen. This angered people from other clans and tribes who saw him as corrupt. A bunch of them turned violent, stormed his house and assassinated him. The tribes then picked Ali ibn Talib, Mohammed's cousin and son in law, to be the fourth Caliph. Uthman's clansmen expected Ali to punish the mutineers, but Ali (who never saw eye to eye with Uthman) adopted a policy of reconciliation. This lead Muwaiyyah ibn Abu Sufyan, Uthman's clansman and governor of Syria, to declare rebellion and appoint himself Caliph.

After several battles, the two Caliphs agreed to end hostilities and resort to arbitration. A group of Ali's supporters saw this as evidence that both men had lost their way, and that it was now their religious duty to depose these corrupt Caliphs, including their former master Ali. This group became known as the Khawarij. Ali defeated them at the battle of Nahrawan, but a few survived. Of the survivors three planned to assassinate Ali, Muwaiyyah and Amr ibn al Aas (governor of Egypt and the appointed arbitrar). Only one of them succeeded, the one targeting Ali.

The Khawarij, now a religious sect, would continue to reappear to rebel against various Caliphs. They never completely disappeared and are believed to be the predecessors of the Ibadi sect which mostly resides in Oman.