His Difficulties

Initial ones

Now no one remained neutral. There were factions now some were pro-Ali, or pro-Usman, or later pro-Muawiyah.
No consensus existed. Ali’s election was more contentious than Usman’s. The Bedouin tribes lying along the outskirts were growing provocative. They knew the state was weakening with each day.
A demand arose that Usman’s murderers must be punished. But Ali was reluctant to do so. There is no clear reason as to why he didn’t want to do so.
He argued it was tough to identify the killers and he couldn’t kill thousands that had marched on Madinah, for that would only lead to more chaos.
But it was a mistake, had he done only enough or started doing initially, he would’ve had support of at least the ones that were neutral in the start.
Several companions were disenchanted, they grew wary. The first chief ones to defect and rebel were Talha, Zubayr, and Ayesha.

Dismissal of Usman’s Governors

Ali believed it was Usman’s lavish-living and unjust governors who had led to present situation. He set out to fire and then replace them all with his choice.
His kinsmen and friend advised him against the action. They maintained it would only lead to more rebellion against him. The Ummah was already divided and this would further weaken it.
Few governors had strict and frim control over their territory such as Muawiyah. Syria didn’t join rebellion since Muawiyah was an able administrator and a general.
Ali finally sent his-chosen governors to main provinces. Some found easy success, and some had to work hard and persuade the populace. But some returned empty-handed such as Suhayl from Syria.

Showdown between Ali and Muawiyah

As noted earlier, Muawiyah was an able administrator and belonged to Umayyad clan. He was pro-Usman and so was majority of Syria. Muawiyah used to arouse people to avenge Usman’s murder.
A blood-stained shirt of Usman was hanged in the city and reminded everyone of rebel’s atrocity and Ali’s reluctance.
Ali wrote letter to him to ask for his allegiance, but he didn’t reply for weeks.
In Syria, a cry was raised to march on Madinah. In 656, Muawiyah replied to the letter. He sent the letter blank with his name on it in bold letters. Ali opened the letter but was baffled why was it empty. The messenger told him of conditions of Syria and how 60k Syrians were mourning Usman’s death and resolved to avenge him.
Ali also raised a force of 40k men. But there he heard about rebellion stemming out Makkah and moving towards Basra. The rebellion was led by Talha, Zubayr, and Ayesha. He turned his army towards Basra to face an immediate threat.

War against Talha, Zubayr, and Ayesha

Besides Umayyads, Ayesha was the first one to reach Makkah. She had gone to Makkah for pilgrimage. While she was returning to Madinah, she heard about the situation in Madinah and resolved to return to Makkah.
Sometimes later Talha and Zubayr also came to Makkah presumably on the pretext of pilgrimage.
Everyone was crying for revenge. At last, it was concluded that army would march on Basra with 3000 men initially.
It is said that Talha and Zubayr had their own motives to reign the State. They had even asked Ali for governorship of Kufa and Basra but were denied by Ali.
When the army reached there, the pro-Usman group defected to Makkan army. The governor of Basra, Usman bun Hanif charged Talha and Zubayr of treachery and reminded them of their homage. They contended they were forced to do so under duress.
A deputation was sent to Madinah to observe if what Talha and Zubayr were saying was true. The deputation returned but with mixed results that leaned a bit on their side. Usman bin Hanif left Basra and fled to Madinah.
Ayesha, Talha, and Zubayr entered Bara and kept their promise and put 600 men to death, who had taken part in rebellion.
Ali was to march to Basra with 20k men that included men from Kufa. Droves of them belonged to faction that taken part in Usman’s killing.
Ali was reluctant to fight Muslims and started negotiating for peace. The other side too was ready to negotiate.
The rebels in Ali’s party knew if the negotiations succeeded the rebels would either be exiled or put to death. The conspirators then attacked Ayesha’s army’s camps. Fighting ensued.
Ali was shocked to see and claimed that he had nothing to do with it but by then anger had taken over soldiers and fierce battle continued.
The battle was won by Ali, but in practice this battle further weakened his position. Ayesha remained unhurt.
The battle that 40k participants lost 10k men. It came to be known as the Battle of Camel (Battle of Jamal).
Ali stayed in Basra for few days and then went to Kufa and made it his capital. This further alienated tribes near Madinah. They believed Ali sure favored the killers of Usman.

For complete Islamic history notes click here.