As long as the umpires had not given their decision at Dumatul Jandal, and a true obtained between Ali and Muawiyah did not interfere directly in the affairs of Egypt. He, however, indirectly helped the pro-Othman group in Egypt led by Muawiyah b Hudaij to maintain their stand against the government of Muhammad b Abu Bakr. At Dumatul Jandal, Abu Musa Ashari declared the deposition of Ali and Amr b Al A'as declared for the sovereignty of Muawiyah. This decision, however, reached and howsoever perverse turned the tables on Ali. The implication of the decision was that, henceforward, Muawiyah was the legitimate ruler of the Muslim state, and Ali was the status of a usurper or a rebel against the legitimate authority, in accordance to propaganda of Muawiyah and 'Amr b Al-A'as, Muawiyah had promised the governship of Egypt to Muawiyah. After 'Amr b Al-A'as had, by a clever trick, conferred the sovereignty on Muawiyah, Muawiyah commissioned 'Amr b Al-A'as to conquer Egypt. When 'Amr departed at the head of on army on the expedition of Egypt Muawiyah said to him, "Amr you were the first conqueror of Egypt, go and reconquer Egypt. "The plan of the pro-Othman party was that while Muawiyah would attack Muhammad b Abu Bakr in Egypt itself, 'Amr should lead the attack from across the borders.
When Ali had originally planned an expedition to Syria, Muhammad b Abu Bakr had a sizable force at his disposal and he could deal with an internal rebellion. When after the Battle of Nahrawan, Ali had to abandon his expedition to Syria, Muawiyah increased his pressure against Egypt. Under the change circumstances many warriors of the forces of Muhammad b Abu Bakr abandoned his cause and either joined the pro-Othman party or preferred to be neutral and keep aloof from the struggle. Muhammad b Abu Bakr was left with a small force of four thousand person only when Muawiyah and 'Amr b Al-A'as launched their offensive. Muhammad b Abu Bakr requested Ali to send him help. Accounts in this respect vary. According to one account Ali because of the non-cooperation of the people of Kufa could not send help but it was insignificant. According to yet another account whatever reinforcement was sent arrived in Egypt, after all was over and Egypt had been captured in the name of Muawiyah. The force which Muhammad b Abu Bakr fought desperately and heroically, but they were cut to pieces by the superior forces of the enemy. After Bashr b Kinana had been killed, and further resistance became impossible, Muhammad b Abu Bakr escaped from the battlefield, and sought refuge in the ruins outside the city of Fustat. Muawiyah secured the countryside and Muhammad b Abu Bakr was taken captive and brought to Fustat. Abdul Rahman b Abu Bakr waited on 'Amr b Al-A'as and pleaded for the life of Muhammad b Abu Bakr 'Amr b Al-A'as send word to Muawiyah that the prisoner should be sent to him. Muawiyah b Hudaij said that he taken to arms in vengeance for the blood of Othman, and he could not show any mercy to the person who was guilty of the murder of Othman. Muhammad b Abu Bakr asked for water from his captors. He was told that he had refused water to Othman, thus no water could be allowed to him. Muhammad b Abu Bakr was mercilessly slain. His corpse was the wrapped in the skin of an ass and burnt.