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On June 17 656 Ali was chosen as Kalief of Islam. A Kalief or Caliph is the chief Muslim civil and religious ruler, regarded as the successor of Muhammad
Ali was the caliph between 656 and 661 CE, one of the hardest periods in Muslim history, coinciding with the first Muslim civil war. He reigned over the Rashidun empire which extended from Central Asia in the east to North Africa in the west. He became known as a both just and fair ruler.
Abu Talib, father of Imam Ali was the among first to convert to islam. He offered care and protection to prophet at his young age after being orphaned at his house.After the assassination of the third Caliph, Uthman Ibn Affan, at the close of the Siege of Uthman, the election of a new Caliph encountered difficulties. The rebels, comprising Muhajerin, Ansar, Egyptians, Kufans and Basntes, and the Kharijites, were divided between three candidates: Ali, Talhah and Al-Zubayr. First they referred to Ali and asked him to accept the caliphate. Also some Companions of Muhammad tried to persuade him to accept the office. But he refused and answered:’Leave me and seek someone else. We are facing a matter which has (several) faces and colors, which neither hearts can stand nor intelligence can accept. Clouds are hovering over the sky, and faces are not discernible. You should know that if I respond to you I would lead you as I know and would not care about whatever one may say or abuse. If you leave me then I am the same as you are. It is possible I would listen to and obey whomever you make in charge of your affairs. I am better for you as a counselor than as chief.’
Then rebels offered the caliphate to Talhah and Al-Zubayr and some other companions but they refused it too. Therefore, they threatened that, unless the people of Medina choose a caliph within one day, they would be forced to take some drastic action. In order to resolve the deadlock all of the Muslims gathered in Mosque of Prophet on 18 June 656CE. (25th Dhu al-Hijjah 35AH.) to choose the caliph. Ali refused to accept caliphate by the fact that the people who pressed him hardest were the rebels, and he therefore declined at first. When the notable companions of Muhammad as well as people who live in Medina urged him, however, he finally agreed. According to Abu Mekhnaf‘s narration Talhah was the first prominent companion who gave his pledge but the other narrations claim they didn’t do so or even somebody forced them to do so. However he and Al-Zubayr later claimed they did so reluctantly, but Ali refused this claim and said that they did so voluntarily. Mudelong believe that force was not used to urge people to give their pledge and they pledged in public in the mosque. 
While the overwhelming majority of people who lived in Medina as well as rebels gave their pledge, some major figures did not. Umayyads, kins of Uthman, escaped to Levant or remained in their houses and later refused Ali’s legitimacy. Sa`ad ibn Abi Waqqas were absent and Abdullah ibn Umar abstained from offering his allegiance but both of them assured Ali that they wouldn’t do anything against Ali.  Another prominent figure who was in Mecca at that time and later opposed Ali, was A’isha, Muhammad’s widow.
At the beginning Ali told people that Muslim polity had come to be plagued by dissension and discord and he wanted to purge Islam of all evil from which it had come to suffer. Then warned all concerned that he would tolerate no sedition and all found guilty of subversive activities would be dealt with harshly. He advised people to behave as true Muslims.
But he soon found that he was helpless and the prisoner of the people who didn’t obey him. The caliphate had come to him as the gift of the rebels and he didn’t have enough force to control or punish them. When some people asked Ali to punish those who killed Uthman, Ali answered, “How do I have the power for it while those who assaulted him are in the height of their power. They have superiority over us, not we over them.” While A’isha, Talhah, Al-Zubayr and Umayyad especially Muawiyah I wanted to take revenge for Uthman’s death and punish the rioters who had killed him. However some historians believe that they use this issue to seek their political ambitions due to finding Ali’s caliphate against their own benefit.
Soon after Ali became caliph, he dismissed provincial governors who had been appointed by Uthman, and replaced them with trusted aides. He acted against the counsel of Mughrah ibn Shobah and Ibn Abbas, who had advised him to proceed cautiously. Madelung says Ali was deeply convinced of his right and his religious mission, unwilling to compromise his principles for the sake of political expediencey, ready to fight against overwhelming odds. Muawiyah, kinsman of Uthman and governor of Levant refused to submit to Ali’s orders – the only governor to do this.
Ali resumed the land which had been granted by Uthman and swore to resume whatever some elites had taken before him. He opposed the centralization of capital control over provincial revenues and favored an equal distribution of taxes and booty among the Muslims; in contrast to Umar he distributed the entire revenue of the divan among Muslims without keeping anything in reserve. When asked to pay more money to elites he said “Do you command me that I should seek support by oppressing those over whom I have been placed? By Allah, I won’t do so as long as the world goes on, and as long as one star leads another in the sky. Even if it were my property, I would have distributed it equally among them, then why not when the property is that of Allah.”
Ali believed that people and governors have rights over each other and God created these rights so as to equate with one another. The greatest of these rights that Allah has made obligatory is the right of the ruler over the ruled and the right of the ruled over the ruler. If the ruled fulfill the rights of the ruler and the ruler fulfills their rights, then right attains the position of honor among them, the ways of religion become established, signs of justice become fixed and the sunnah gains currency. He wrote directions for his officials which clearly show what form of regime he wanted to introduce. It was not to be a regime whose officers had an upper hand and were fattened on public money. It was to be a regime where the governed and the tax-payers were at premium. It was their convenience for which the State was to function. It was a welfare-state working solely for the welfare of the people living under its rule, a regime where the rich cannot get richer while the poor are made poorer; a regime where canons of religion hold the balance between the governed and the ruler. He asked people not to speak with him as they spoke with cruel governors and be honest with him.
Ali had decisive beliefs that he shouldn’t start a war with other Muslims but when the enemy started it his army wouldn’t retreat unless they wanted to attack again. He ordered his soldiers not to kill who would become injured, or not be able to defend himself, or escape from the battlefield and injuries and wanted his warriors not to injure women