It appears that the Ismaili ruler of Gilgit, Raja Trakhan (1310-1335) was succeeded by Raja Somul (1335-1390). The third ruler was Raja Khusaro Khan (1390-1435), then Raja Hyder Khan (1435-1480), Raja Chalis Khan (1480-1515) and Raja Nur Khan (1515-1565). It means that the Ismailis ruled Gilgit absolutely for about 255 years. But, the seventh ruler Raja Mirza Khan (1565-1600) was invaded by Ali Sher Khan Anchan (1595-1633), the ruler of Skardu. Raja Mirza Khan took flight to Baltistan and lived as a refugee with the Maqpon ruler, Raja Ghazi Mir (1565-1595), who had died a month later. Raja Mirza married to the daughter of the ruler, and became a Twelver. He took field against Gilgit with colossal means and materials he acquired from the new ruler, Raja Ali Sher Khan (1600-1632), and subdued Ali Sher Khan Anchan at Gilgit, and reinstated his rule. Henceforward, he forced the inhabitants to follow the doctrines of the Twelver. The Ismailis observed strict taqiya, and were also known as the Mughli.
Imam Khalilullah Ali I died at Kahek in 993/1585, but he was buried in Anjudan. It seems that the Ismailis were thickly populated in Anjudan, therefore, it was resolved to settle few families in Kahek in Kirman. According to another tradition, the Twelvers and Nuqtawiyas also lived in Anjudan and its locality, therefore, the governor of Hamdan had appointed a certain Shia leader, called Sayed Khalilullah as the amir of Anjudan after Imam's departure from the village in 992/1584. An epigraph discovered by Farhad Daftary at Anjudan is allegedly collated with the preceding move. It reproduces the text of a royal edict issued by Shah Abbas II in Rajab, 1036/March-April, 1627 addressing to amir Khalilullah Anjudani, for the exemption of certain taxes, wherein the Anjudani Shias are explicitly regarded as the Twelvers. Farhad Daftary however identifies Amir Khalilullah Anjudani as Imam Zulfikar Ali, who was also known as Khalilullah. The balance of arguments points that it is almost a tentative speculation, and nothing to do with historical fact.
It is worth mentioning that the "Tarikh-i Alfi" (the Millennial History) was compiled in India by several authors at the request of Mughal emperor Akbar in 1000/1592, whose one part was chronicled by Jafar Beg Asif Khan (d. 1021/1612), describing a rebellion hatched by a certain Murad under the year 982/1575 and the domineering of the Ismailis in Anjudan by Shah Tahmasp (d. 984/1576). More details of the same episode is described under the year 981/1574 by the Safavid historian, Qadi Mir Ahmad Munshi al-Qummi (d. after 1015/1606) in his "Khulasat al-Tawarikh" (1st vol., pp. 582-4). Both sources relate that a certain Murad had numerous followers also in India, sending him large sums of money from Sind and Makran. Murad was engaged in political turmoil outside Anjudan, having acquired supporters in Kashan and elsewhere in Central Iran. Being alarmed by his activity, early in 981/1574, Shah Tahmasp ordered the Kizilbash governor of Hamdan, Amir Khan Mawsil'lu, to take field against Anjudan and arrest Murad. Amir Khan executed a bulk of the Ismailis in Anjudan and its locality and took much booty from them, but Murad, who was stayed at a fortress in the district of Kamara near Anjudan, managed to escape. Soon afterwards, Murad had been arrested and imprisoned near the royal quarters. In Jamada II, 981/October, 1573, Murad escaped from prison with the help of Muhammad Muqim, a high Safavid official who had come under Murad's influence. Murad fled to the vicinity of Kandhar, getting help on the way from his followers in Fars, Makran and Sind. A few months later, he was arrested in Afghanistan by the Safavid guards. He was brought before Shah Tahmasp, who had him executed along with Muhammad Muqim.
Farhad Daftary bluntly hazards to identify above certain Murad with Imam Murad Mirza (d. 920/1514), which seems that he is explicitly divorced from reality. The most important aspect of the story which deserves serious treatment is the stark difference between these two persons for about 60 years. Secondly, it is neither warranted in the Ismaili traditions, nor there is a single example, connoting the Imams to have involved in the political arena while living in Anjudan, and therefore, the alleged rebellion of the Imam Murad Mirza is highly doubtful. Thirdly, it would be absurd to believe that the Imam Murad Mirza had vainly stirred up a revolt with handful supporters and fled, putting behind his followers into the millstone of cruelty in Anjudan. Fourthly, the remittance of religious dues to the Imams by the Indian followers was an practice in vogue, which can be incorporated to suit the notion of any anecdote for the Ismailis. Fifthly, the above story places the rebellion in 982/1575, which is veritably the period of Imam Khalilullah Ali (957-993/1550-1585), the last Imam of Anjudan era. We would, however, venture the opinion that the whole story embodies elegance and rhetoric rather than a factual picture, and that Mirza in the story was in reality the leader of the Nuqtawiya sect in the time of Imam Khalilullah. He mustered a handful supporters for engineering a ground of rebellion against the Safavids. The followers of the Nuqtawiya were inhabited in the vicinity of Anjudan, and their uprising under their leader, Murad cannot be attributed to the Ismailis. It seems unlikely, therefore, that Imam Murad Mirza was that of a rebellious Murad.
It must be added on this juncture that several extremist movements with Shiite tendencies sprouted in Iran. For instance, the Hurufi movement was founded by a certain Fazalullah Astrabadi (740-796/1340-1394) in about 780/1378. His followers became known as Hurufis due to emphasizing the hidden meaning of the letters (huruf). Anatolia was the main foothold of the Hurufism. Later on, the Hurufism vanished in Iran, and several petty groups split off from it, notably the Nuqtawiya. It was founded by Mahmud (d. 831/1428) around 800/1398, who was the disciple of Fazalullah Astrabadi in Gilan. Mahmud taught to his followers the significance of the point (nuqta) as the building brick of his symbolical system. Thus, his group became known as the Nuqtawiya (pointism) and his followers as the People of the Point (ahl-i-nuqta). The Nuqtawiya gradually found their foothold in the Caspian region and the villages of Qazwin, Kashan, Ispahan and Shiraz. Mahmud died in 831/1428 on the border of Azerbaijan and Arran. His followers however continued his mission in Iran and India.
Our sources as cited above also relate a revolt under the year 983/1576 by the followers of Mahmud against the Safavids in the village surrounding the city of Kashan. This major revolt occurred in conjunction with an uprising in Anjudan led by the Nuqtawiya leader, called Murad. "Tarikh-i Alfi" admits specifically that the revolt stirred in Anjudan by Murad was that of the Nuqtawiya order.
We also find a vogue tendency in the Iranian sources to conflate the Hurufis and Nuqtawiya wrongly with the Ismailis. The instance of an Ismaili poet, Kassim Amiri is ample in this contex, who was lynched in 999/1591. He is considered erroneously as the follower of the Nuqtawism in the Iranian sources. Ahmad bin Nasrullah Qadizada Tatawi, whose father had taken part in suppressing the Kashan revolt, was vague about the connection between the two revolts, suggesting explicitly that the followers of Mahmud were collaborating with the Ismailis of Anjudan, vide "Nuqtawiyan ya Pisikhaniyan"(Tehran, 1941, p. 36) by Sadik Kiya.
The balance of argument tends to show in concluding this critique that Imam Murad Mirza had nothing to do with the above rebellion of the Nuqtawiya.