From Basra, Ali did not proceed to Madina. He proceeded to Kufa instead. When Ali had sent a mission to Kufa to get volunteers for the fight against Basra, he had promised the people of Kufa that would make their city the capital of the caliphate. After his victory of Basra, Ali declared Kufa to be the capital of the Muslim Commonwealth. When Ali had left Madina for his campaign against Talha and Zubair little did he imagine that he was not destined to visit Madina again.
After winning the victory at Basra, Ali came to feel that as he had won a victory at Basra against Ayesha, Talha and Zubair, so would he be able to win a victory against Muawiyah. For a campaign against Syria, the response from the people of Madina had been poor. As the people of Madina were religiously more advanced they were averse to side with any party for an armed conflict among the Muslims. Some eminent companions in Madina had even abstained from taking the oath of allegiance to Ali, and had preferred to follow a policy of neutrality. As such Ali felt that for any confrontation with Muawiyah, Madina could not serve as a base.
When Othman had been assassinated, the rebels had violated the sanctity of the holy city of the holy Prophet. Ali was accordingly of the view that in order to preserve the sanctity of the holy city of Madina, it was expedient that the political capital should be shifted elsewhere so that the sacred city should be spared the ordeals of facing political storms.
In the campaign against Basra, Ali had succeeded in raising a large force from Kufa. Ali hoped that after the victory of Basra, the prospects of raising a still larger force from Kufa for the campaign against Syria would be brighter. Geographically Kufa was more centrally located, and a war against Syria could be carried more advantageously with the base at Kufa instead of Madina. Those considerations prompted Ali to establish his capital at Kufa.