The Turks very naturally wished to regain control in their province Egypt, which meant that they desired to crush the independent spirit of the Mamluwk chieftains whose authority was once recognized by the Egyptians but under these new circumstances was seriously undermined.

 The British Government now made representations to the Porte (al-Bab al-`Aliy), urging a tolerant treatment of the Mamaliyk but in spite of this the Turkish admiral, having invited a number of these chieftains to a fête (feast) upon his flagship, treacherously fired upon them while they were coming to him in open boats, and killed or captured them all. General Hely Hutchinson, the British commander, was furious at this outrage, which had taken place almost under his eyes; and as a result of his protest the prisoners were handed over to his care. At the same time, the Turkish general in Cairo arrested as many of the remaining chieftains as he could lay hands on; but the British forced him to give them up. Not long after this, Khusruw Pasha, with 7000 Turks, attacked a Mamluwk force of 800 men commanded by two famous chieftains, `Uthman al-Bardiysiy and Muhammad al-'Alfiy.  However, his large force was utterly routed, and the`Uthmanliy (Ottoman) hold on Egypt was thereby greatly diminished.
 

Muhammad`Aliy  now began to realize that he was fighting on the losing side, for the Mamaliyk had every reason to be confident both in their own strength and in the support of the British; and he therefore showed an inclination to abandon the Turkish cause. In March 1803,  however, the British army evacuated the country, taking with them to England the Mamluwk chieftain al-'Alfiy, who was to consult the Home Government as to the best method of reestablishing control over Egypt under Mamluwk rule, with English supervision. Muhammad`Aliy, therefore, was left to decide which side to take; and it was not long before he showed in which direction he believed his best interests to lie.
 

 About six weeks after the departure of the British army, the entire Albanian force in Egypt, commanded by Tahir Pasha, to whom Muhammad `Aliy was lieutenant, came to blows with the Turkish Governor, Khusruw Pasha, in regard to their pay. They seized the Citadel at Cairo, and from this eminence bombarded the Governor in his palace in the al-'Izbakiyah, a low-lying district at that time near the western outskirts of the city. Khusruw managed to escape by river to Dumiyat (Damietta); and Tahir was proclaimed Governor in his stead. Less than a month later he, in his turn, found himself unable to pay his troops; and by one of those remarkable maneuvers, of which we have already noticed two previous instances, Muhammad `Aliy managed to obtain the chief command, after Tahir mysteriously died.

The appointment of this representative of the Porte (al-Bab al-`Aliy) was regarded by Muhammad `Aliy simply as a means of holding the post open for himself, as soon as he should have opportunity to bring his authority before the notice of the Porte  (al-Bab al-`Aliy) ; for he now aimed at nothing less than the complete control of Egypt. He had no intention of remaining in alliance with the Mamaliyk when once his own position was secure; and he felt that his policy should be directed towards rapprochement with Turkey.

In the spring, an open rupture occurred between him and the Mamluwk chieftains, owing, as usual, to a question of the payment of the troops; and on March 12, 1804, Muhammad `Aliy attacked al-Bardiysiy in his palace and drove him out of Cairo. The Cairenes and Albanians then invited Khuwrshid Pasha, the Turkish Governor of Alexandria, to assume the governorship of their city; but this individual, wishing to be secure against the domination of Muhammad `Aliy's troops, introduced a regiment of al-Magharibah (North Africans) into the city, stationing them in the Citadel, and thereby incurred the Albanian's furious displeasure.

About a year later, therefore, Muhammad `Aliy persuaded the Cairenes to depose Khuwrshid and to nominate himself as Governor of Cairo, Khuwrshid very naturally refused to recognize any nomination not confirmed by the Sultan, and promptly turned the guns of the Citadel upon Muhammad `Aliy's forces in the town below. The energetic Albanian replied by dragging his cannons up to the summit of the Muqattam hills, which dominated the Citadel, and meanwhile he sent an embassy post-haste to Istanbul asking for the official deposition of his enemy. The document arrived in Cairo on July 9, 1805, and a Turkish force was sent to restore order. Khuwrshid then surrendered, and Muhammad `Aliy assumed the governorship, having attained this exalted position at the early age of thirty-six.