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[42] 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[43] and began in reality a major transformation of a "revolutionary" nature which caused him innumerable difficulties.[44]
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."[45]
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.
The first group were among the elite of the companions of the Holy Prophet and among the ascetics, devout worshipers and selfless devotees of Islam who struggled on the path of Islamic freedom. They were especially loved by the Prophet. The Prophet said,
"God has informed me that He loves four men and that I should love them also." They asked about their names. He mentioned Ali and then the names of Abu Dharr, Salman and Miqdad. (Sunan of Ibn Majah, Cairo, 1372, vol.I, p. 66.) 'A'ishah has recounted that the Prophet of God said, "If two alternatives are placed before Ammar, he will definitely choose that which is more true and right." (Ibn Majah, vol. I, p. 66.) The Prophet said, "There is no one between heaven and earth more truthful than Abu Dharr." (Ibn Majah, vol. I, p. 68.) There is no record of a single forbidden act committed by these men during their lifetime. They never spilled any blood unjustly, did not commit aggression against anyone, did not steal anyone's property, never sought to corrupt and misguide people.
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.
The first war in the caliphate of Ali, which is called the "Battle of the Camel," was caused by the unfortunate class differences created during the period of rule of the second caliph as a result of the new socioeconomic forces which caused an uneven distribution of the public treasury among members of the community.
When chosen to the caliphate, Ali divided the treasury evenly[46] as had been the method of the Holy Prophet, but this manner of
dividing the wealth upset Talhah and Zubayr greatly. They began
to show signs of disobedience and left Medina for Mecca with the
alleged aim of making the pilgrimage. They persuaded "the
mother of the Faithful" (umm al-mu'minin), A'ishah, who was not
friendly with Ali, to join them and in the name of wanting to
revenge the death of the third caliph they began the bloody Battle
of the Camel.[47] This was done despite the fact that this same
Talhah and Zubayr were in Medina when the third caliph was
besieged and killed but did nothing to defend him.[48] Furthermore, after his death they were the first to pay allegiance to Ali on behalf of the immigrants (muhajirun)[49] as well as on their own.[50]
Also, the "mother of the Faithful," A'ishah, did not show any opposition to those who had killed the third caliph at the moment when she received the news of his death.[51] It must be remembered that the main instigators of the disturbances that led to the death of the third caliph were those companions who wrote letters from Medina to people near and far inviting them to rebel against the caliph, a fact which is repeated in many early Muslim histories.
As for the second war, called the Battle of Siffin, which lasted for a year and a half its cause was the covetousness of Mu'awiyah for the caliphate which for him was a worldly political instrument rather than a religious institution. But as an excuse he made the revenge of the blood of the third caliph the main issue and began a war in which more than a hundred thousand people perished without reason. Naturally, in these wars Mu'awiyah was the aggressor rather than the defender, for the protest to revenge someone's blood can never occur in the form of defense. The pretext of this war was blood revenge. During the last days of his life, the third caliph, in order to quell the uprising against him, asked Mu'awiyah for help, but the army of Mu'awiyah which set out from Damascus to Medina purposely waited on the road until the caliph was killed. Then he returned to Damascus,to begin an uprising to revenge the caliph's death.[52] After the death of Ali and his gaining the caliphate himself, Mu'awiyah forgot the question of revenging the blood of the third caliph and did not pursue the matter further.
After Siffin there occurred the battle of Nahrawan in which a number of people, among whom there could be found some of the companions, rebelled against Ali, possibly at the instigation of Mu'awiyah.[53] These people were causing rebellion throughout the lands of Islam, killing the Muslims and especially the followers of Ali. They even attacked pregnant women and killed their babies. Ali put down this uprising as well, but a short while later was himself killed in the mosque of Kufa by one of the members of this group who came to be known as the Khawarij.
The opponents of Ali claim that he was a courageous man but did not possess political acumen. They claim that at the beginning of his caliphate he could have temporarily made peace with his opponents. He could have approached them through peace and friendship, thus courting their satisfaction and approval. In this way he could have strengthened his caliphate and only then turned to their extirpation and destruction. What people who hold this view forget is that the movement of Ali was not based on political opportunism. It was a radical and revolutionary religious movement (in the true sense of revolution as a spiritual movement to reestablish the real order of things and not in its current political and social sense); therefore it could not have been accomplished through compromise or flattery and forgery. A similar situation can be seen during the apostleship of the Holy Prophet. The infidels and polythesis proposed peace to him many times and swore that if he were to abstain from protesting against their gods they would not interfere with his religious mission. But the Prophet did not accept such a proposal, although he could in those days of difficulty have made peace and used flattery to fortify his own position, and then have risen against his enemies. In fact, the Islamic message never allows a right and just cause to be abandoned for the sake of strengthening another good cause, nor a falsehood to be rejected and disproven through another falsehood. There are many Quranic verses concerning this matter. [54]