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Al-Nizar seems well aware of the domination of al-Afdal, who had a vein of animosity in his character for him. It is possible that he thought it futile to produce the written document in the palace, because according to Ibn Khaldun (4th vol., p. 139) the sister of al- Mustansir had falsely witnessed in the court the story of change of nass, therefore, he did not come back to the palace and quitted Cairo. Soon afterwards, al-Nizar appeared at Alexandria, supported by his brother, Abdullah and an amir, Muhammad ibn Massal al-Maliki. Nasir ad-Dawla Iftagin at-Turki, the governor of Alexandria swore allegiance to al-Nizar and proclaimed his support. Jalal ad-Dawla bin Ammar, the qadi of Alexandria also supported the cause of al-Nizar. In Alexandria, al-Nizar promulgated the Nizarid Ismaili mission and adopted the title of al-Mustapha li-dinillah (the chosen for God's religion).
Nasir Khusaro and Hasan bin Sabbah were promulgating the Nizarid Ismaili mission in Badakhshan and Iran in accordance with the directions they had personally received from al-Mustansir when they had been in Cairo. Granted that the theory of change of nass was a genuine, then these missionaries must have been intimated by the Fatimid authority, but it was produced only in the court as a tool to make al-Musta'li enthroned.

Al-Afdal feared the growing power of al-Nizar in Alexandria, where he spurred his horses in 488/1095, but suffered a sharp repulse in the first engagement, and retreated to Cairo. According to Ibn Athir and Ibn Khallikan, al-Nizar also got favour of the nomad Arabs and dominated the northern area of Egypt.

Al-Afdal once again took field with huge army and besieged Alexandria. He tempted the companions of al-Nizar, and fetched them to his side. Ibn Massal was the first to have deserted the field from the thick of fight, and fled with his materials by sea towards Maghrib. It is related that Ibn Massal had a dream that he was walking on horseback, and al-Afdal was walking in his train. He consulted an astrologer, who remarked that he who walked on the earth was to possess it. On hearing this, Ibn Massal collected his wealth and fled to Lokk, a village near Barqa in Maghrib. This defection marked the turning point of al-Nizar's power. In addition, the long siege resulted great fortune to al-Afdal, wherein many skirmishes took place. Al-Nizar and his faithfuls fought valiantly, but due to the treachery of his men, he was arrested and taken prisoner with Abdullah and Iftagin to Cairo.

Iftagin was executed in Cairo. According to Ibn Khallikan, al-Nizar was immured by his brother al-Musta'li's orders and al-Afdal had him shut up between two walls till he died in 490/1097. According to John Alden Williams in 'Islam' (New York, 1967, p. 218), 'The followers of al-Nizar in Abbasid territory refused to accept this and took Nizar's son to one of their mountain fortress, Alamut.'

The Ismaili missionaries spread the Nizari Ismailism since the time of al-Mustansir by leaps and bounds. Hasan bin Sabbah had operated the Nizarid mission freely throughout its length and breath and established the Nizarid rule at Alamut in Iran. Henceforward, the centre of the Nizari Imamate with a large following in Iran, Syria and Central Asia, transferred from Egypt to Iran.

Muhammad bin Ali al-Suri, the Fatimid dai in Syria, who died few months after al-Mustansir billah in 488/1095, had enumerated the Imams in a long Arabic poem, vide 'al-Qasida al-Suriyya' (ed. Arif Tamir, Damascus, 1955, pp. 41-71). He is said to have given his full supports to the cause of al-Nizar in Syria and propagated to this effect in his region.

According to Ibn Khallikan, Ibn Massal received a letter from al-Afdal, inviting him to return to Egypt, which he did, and was honourably received in Cairo.

Al-Musta'li remained a puppet in the hands of al-Afdal throughout his short reign (1094-1101), during which the Crusaders first appeared in 490/1097 in the Levant to liberate the holy land of Christendom. The Crusaders easily defeated the local Fatimid garrison, and occupied Jerusalem in 492/1099. By 493/1100, the Crusaders had gained their footholds in Palestine, and founded several principalities based on Jerusalem and other localities in Palestine and Syria. In the midst of the Fatimids' continued attempts to repel the Crusaders, al-Musta'li died in 495/1102, who made no personal contribution to the Fatimid rule. He was entirely without authority in the state, and came out only as required by al-Afdal at the public functions.

W.B. Fisher writes in 'The Middle East and North Africa' (London, 1973, p. 243) that, 'After the death of al-Mustansir, the six succeeding caliphs had no power'. After Musta'li's death, al-Afdal proclaimed al-Musta'li's five year-old son, Abu Ali al-Mansur, surnamed al-Amir (d. 524/1130).