The caliphate of Ali began toward the end of the year 35/656 and lasted about four years and nine months. During his period as caliph Ali followed the ways of the Holy Prophet  and brought conditions back to their original state. He forced the resignation of all the incompetent political elements who had a hand in directing affairs  and began in reality a major transformation of a “revolutionary” nature which caused him innumerable difficulties. 
On his first day as caliph, in an address to the people, Ali said, “O People, be aware that the difficulties which you faced during the apostolic period of the Prophet of God have come upon you
Once again and seized yow. Your ranks must be turned completely around so that the people of virtue who have fallen behind should come forward and those who had come to the fore without being worthy should fall behind. There is both truth (haqq) and falsehood (batil). Each has its followers; but a person should follow the truth. If falsehood be prevalent it is not something new, and if the truth is rare and hard to come by, sometimes even that which is rare wins the day so that there is hope of advance. Of course it does not occur often that something which has turned away from man should return to him.”
Ali continued his radically different type of government based more on righteousness than political efficacy but, as is necessary in the case of every movement of this kind, elements of the opposition whose interests were endangered began to display their displeasure and resisted his rule. Basing their actions on the claim that they wanted to revenge the death of Uthman, they instigated bloody wars which continued throughout almost all the time that Ali was caliph. From the Shi’ite point of view those who caused these civil wars had no end in mind other than their own personal interest. The wish to revenge the blood of the third caliph was no more than an excuse to fool the crowd. There was no question of a misunderstanding.
After the death of the Holy Prophet, a small minority, following Ali, refused to pay allegiance. At the head of the minority there were Salman, Abu Dharr, Miqdad, and Ammar. At the beginning of the caliphate of Ali also a sizable minority in disagreement refused to pay allegiance. Among the most persistent opponents were Sa’id ibn ‘Ass, Walid ibn ‘Uqbah, Marwan ibn Hakam, ‘Amr ibn ‘Ass, Busr ibn Artat, Samurah ibn Jundab, and Mughirah ibn Shu’bah.
The study of the biography of these two groups, and meditation upon the acts they have performed and stories recounted of them in history books, reveal fully their religious personality and aim.
History is, however, full of accounts of unworthy acts committed by some of the second group. The various acts committed by some of these men in opposition to explicit Islamic teachings are beyond reckoning. These acts cannot be excused in any manner except the way that is followed by certain groups among the Sunnis who say that God was satisfied with them and therefore they were free to perform whatever act they wished, and that they would not be punished for violating the injunctions and regulations existing in the Holy Book and the Sunnah.
1. Editor’s note: The title amir al-mu’minin, commander of the faithful,” is used in Shi’ism solely for Ali, whereas in Sunni Islam it is a general title conferred upon all the caliphs.
2. Ya’qubi, vol.ll, p.154.
3. Ya’qubi; vol.ll, p.155; Muruj al-dhahab, vol.ll, p.364.
4. Editor’s note: Revolutionary in this context does not of course bear the same meaning that it carries generally today. In a traditional context a revolutionary movement is the reestablishment or reapplication of immutable principles of a transcendent order whereas in an anti-traditional context it means rebellion against either these principles or their application or against any established order in general.
Taken from the book: SHI’A
By Allamah Seyyed Muhammad Hussein Tabatabai