After the departure of the British forces from Kandhar on August 9, 1842 for Quetta, the Aga Khan stayed on in Kandhar for about six weeks with Sardar Sherdil Khan. Rawlinson who sympathised with him, had advised him to retreat to India. Hence, the Aga Khan reached Quetta on October 5, 1842 and then went to stay with the Khan of Kalat, Mir Shahnawaz Khan for more than a month. Before he left, he had been given a letter of recommendation to Sir Charles Napier (1782-1853) by MacNaghten. By the end of November, the Aga Khan reached Sukkur and met Sir Charles Napier, who had been commissioned a general officer to the supreme civil, political and military control of both upper and lower Sind by Lord Ellenborough on August 26, 1842. In January, 1843, the Aga Khan went with Napier to the British camp at Bhiria and then to Hyderabad with his sixty horsemen. In Hyderabad, he was employed in the British service during the battles of Miami and Dubba.
Sind, about 50,000 square miles in extent, had a population of little over a million in the time of the Mirs. H.T. Lambrick writes in "Sir Charles Napier and Sind" (London, 1952, p 14) that, "The great majority of concurred in the opinion that Sind was crushed by the oppressive government of the Mirs, a selfish, ignorant, and bigoted despotism, delibrately calculated to prevent that development of the country which its great natural resources deserved." During the Anglo-Afghan War, the Mirs of upper and lower Sind had allowed the British forces to pass through their territories. In 1840, James Outram was appointed as the British political agent to the Mirs of lower Sind in place of Henry Pottinger. Outram was also made political agent of upper Sind in place of Ross Bell in 1841. Sir Charles Napier held many meetings in December, 1842 and January, 1843 with the Mirs for the negotiations. However, on January 11, 1843, Napier stormed the deserted fortress of Imamgarh. The Baluchi tribes of one of the Mirs were embittered and on February 14, 1843, attakced the British residency in Hyderabad. On February 17, Napier marched with his forces on Hyderabad and defeated the Mirs of Hyderabad, Khairpur and Mirpur in the battle of Miami. The Mirs of upper and lower Sind surrendered except Mir Sher Muhammad of Mirpur. On March 26, 1843, at the battle of Dubba, Napier defeated Sher Muhammad, and the annexation of Sind to the British territories was formally announced on August, 1843. In Sind, the Aga Khan placed his cavalry at the disposal of the British, and tried to convince Nasir Khan, the then Talpur amir of Kalat, to cede Karachi to the British. Nasir Khan refused to cooperate, the Aga Khan disclosed his battle plan to James Outram. As a result, the British camp was saved from a night attack. For his valuable services, the Aga Khan was granted an annual pension of £ 2,000 from Charles Napier with a title of His Highness.