The fall of Alamut must have had a tremendous impact upon the Syrian Ismailis, and greatly impaired their morale. They were now deprived of the leadership and occasional practical guidance formerly given to them from Alamut. The Mongols had constituted befalling and perennial distress to the Ismailis in Syria. During the Mongol's incursion in Syria, the Ismailis were under the leadership of dai Radi al-Din Abul Ma'ali (d. 659/1261), who had punished the Ismaili chiefs who had surrendered their castles to the Mongols. Ibn Muyassar (1231-1278) writes in "Tarikh-i Misar" (p. 68) that, "Radi al-Din had become the chief dai in Syria in 656/1258, and before succeeding to that office, he had gone to Mamluk Egypt as an Ismaili envoy in 655/1257." The Syrian Ismailis established friendly relations with sultan Baybars (658-676/1260-1277). Ibn Abd al-Zahir (d. 692/1293) writes in "Sirat al-Malik al-Zahir" (pp. 138-9) that, "In 659/1261, sultan Baybars granted rights to the Ismaili territories to al-Malik al-Mansur (642-683/1244- 1285), the Ayyubid prince of Hammah." Meanwhile, the Syrian Ismailis sent an embassy to sultan Baybars, demanding successfully the privileges they had enjoyed under the Ayyubids. Baybars appointed Jamaluddin Hasan bin Thabit as the head of the Ismailis in place of Radi al-Din, which was evidently opposed and scourged to death. Radi al-Din died and the aged Najmuddin Ismail bin al-Sharani (d. 672/1274), who was probably above 80 years old, became the head of the Syrian mission in 660/1262. He was later on assisted by his son Shamsuddin and his son- in-law Sarimuddin Mubarak, the son of Radi al-Din. The Syrian Ismailis continued to hold possession of eight strongholds, namely, Masiyaf, Qadmus, Kahf, Khwabi, Rusafa, Maynaqa, Ulayqa and Qulaya.
In 661/1263, when sultan Baybars was engaged in his campaign against the Franks, an Ismaili deputation under Shamsuddin and Sarimuddin is reported to have come to the sultan with gifts. According to "Sirat al-Malik al-Zahir" (comp. in 663/1264) by Ibn Abd al-Zahir (d. 692/1293), "Ambassadors of the Ismailis arrived with presents, and the two sons of the rulers, who were the commanders of the Ismailis, also came; the sultan treated them with kindness, after which they departed." In 664/1265, however sultan Baybars ordered the collection of taxes on the gifts being sent to the Ismailis by the Frankish kings and the ruler of Yamen. Soon afterwards, the Ismailis began to pay tribute to Baybars, following the truce concluded in 664/1266 between the Mamluk sultan and the Hospitallers, the terms of which stipulated that the latter must renounce the tribute hitherto they used to levy upon the Ismailis and other Muslim rulers in the districts of Hammah and Hims. In 665/1267, the Ismailis became tributaries of Mamluk sultan, paying him what was paid previously to the Hospitallers.
In 669/1271, when sultan Baybars was besieging the Frankish castle of Hisn al- Akrad, two Ismaili fidais from Ulayqa were alleged to have joined hands with Bohemond IV of Tripoli to kill sultan Baybars, Thus, Baybars took swift action, and ordered that the stronghold of Ulayqa should be besieged. Ulayqa and Rusafa were reduced at first, and Khwabi, Qulaya, Maynaqa and Qadmus also capitulated in 671/1273. Only the garrison of Kahf mustered some resistance. Having taken the control of the Ismaili territories, sultan Baybars, however tolerated the Ismailis and did not eliminate them. The Ismailis were allowed to exist as loyal subjects of the Mamluks.
Indeed, there are however, some historical reports that sultan Baybars and his successors used to employ the services of the Ismaili fidais against their own enemies, whose benefit was acquired by the Mamluks, and the defamations were put on the Syrian Ismailis. Hence, the Ismaili fidais had been used as an instrument to threaten the enemies of the Mamluks. The historians however have painted it in gloomier colours than it merits. The Mamluk sultan Baybars (d. 676/1277) subjugated the Ismailis since 671/1273, making them devoid of any political significance, and existed as the loyal subjects of the Mamluks and later the Ottoman of Turkey. In sum, with the surrender of Kahf, the last Ismaili castle, on 22nd Zilhida, 671/July 10, 1273 and the elimination of the Ismaili power in Syria, sultan Baybars I completed what Halagu Khan had began in Iran in 654/1256.
The Ismailis in Khorasan and Badakhshan including upper Oxus were relatively not accessible to the Mongol sword during the turbulent period. They continued to develop a distinctive tradition of their own and played prominent role in preserving the Nizari Ismaili literature. It is important to note that the Ismailis of the upper Oxus considered Aziz Nasafi as a co-religionist. He was a celebrated Sufi master and a prolific writer in Central Asia, who later emigrated to Iran and died there around 661/1262. His famous Sufic treatise, "Zubdat al- Haqaiq" (Quintessence of Metaphysical Truth) is preserved still in Badakhshan being an Ismaili work, which was lithographed in Tehran in 1903.
The Indian Nizari Ismailis, designated chiefly by the term Khoja since the time of Pir Satgur Nur, also continued to retain their own traditions under the leadership of local elders in Gujrat until they merged with the growing Ismaili community in India.
The Ismailis in Iran, however, became absolutely disorganized and disoriented immediately with the destruction of their state. Despite the repressions and debacles, the Ismailis' fortune continued to rise gradually in Iran during the turbulent years. Those who managed to survive the Mongol massacres in Rudhbar and Kohistan, had entered a new era of their history. They mostly had taken refuge in obscurity, cloaked by the forms of a Sufi tariqah, and most of them referred to their spiritual leader not as an Imam but as a Pir for many years. The underground existence of the Ismailis in whole Iran did not attract the attention of the historians, who did not have any direct link or approach with them and who, like Juvaini, also wrote that the Mongols had completely extirpated the Nizari Ismailis in Iran. It however appears that many of them had escaped the main brunt of the Mongol onslaughts and did exist in Kohistan, Daylam, Rudhbar etc. A facsimile of a manuscript dating 690/1290 composed by Wahid al-Muluk, unearthed by Sir E. Denison Ross (cf. Royal Asiatic Society, London, 1931, 2nd vol., p. 202), indicating that, "In Persia, the Ismaili communities were decimated by massacre, but survived after the surrender of Alamut and other fortresses in Daylam and Kohistan." Poet Nizari Kohistani (d. 720/1320) very watchfully describes the survival of the Ismailis in Kohistan, Birjand, Rudhbar etc. in his "Kulliyat", a manuscript in the Institute of Language and Literature of the Academy of Science of the Tajik. Mustapha Qazwini compiled his "Nuzhat al-Qulub" in 740/1340 also gives a condensed account of Rudhbar in Mazandaran, whose inhabitants were Ismailis. The Ismailis also lived in Gilan, probably in the mantle of the local Sufis. H.L. Rabino writes in "Rulers of Gilan" (JRAS, 1920, vol., III, p. 294) that, "It is generally believed that the fall of castle of Alamut in 654/1256 marks the end of the Ismaili influence in Gilan. This is a great mistake. Either the destruction of Alamut cannot have a complete as reported by the Persian writers, or the castle was rebuilt."
Yet, Lamasar held out for another year before cholera broke out and killed the bulk of garrison. The few who survived the epidemic had no alternative but to surrender in 655/1258. The valiant garrison of Girdkuh however continued to resist its Mongol besiegers for 13 years after the reduction of Alamut. In the biography of Kuo K'an, the Chinese officer in Mongol forces, it is recorded that Girdkuh was situated on the top of the mountain Tan-han (i.e., Damghan), and was only accessible by ladders, which were guarded by the most valiant troop, vide "Mediaeval Researches from Eastern Asiatic Sources" (London, 1888, 1st vol., p. 122) by E. Bretschneider. In another Chinese source, "Hsi Shin Chi", we find a record of the journey of a Chinese envoy, Chang Te, sent by Halagu in 1259; wherein it is described Girdkuh as a mountain fortress "on a very steep rock, which could not be reached by arrows or stones. The rock was so steep that when one looked up, his cap fell off." Haython however writes in "Flos Historianrum Terrae Orientis" that, "Tigado (Girdkuh) was an impregnable castle, well furnished with all necessaries, and was so strong that it had no fear of attack on any side." At length, the garrison came down not due to starvation, but it was the lack of adequate clothing against the severe winter cold that ultimately broke their spirits. The final surrender reported to have taken place on 29th Rabi II, 669/December 15, 1270.
It has been learnt that when Halagu quitted Iran for his operations against Baghdad, the Ismaili commanders at remote distance had also surrendered their castles upon receipt of official orders without knowing veritable picture. Few among them are reported to have treked in Rudhbar after the massacre of the Ismailis in 656/1257. They made an intensive search of the succeeding Imam after being known locally that Ruknuddin Khurshah had been also killed. With the help of few local fidais, the Ismaili commanders obtained possession of Alamut around 674/1275, about five years after the fall of Girdkuh. The fortress underwent temporary construction and renovation. The reason for re-occupation, as we have been informed, was to give an inkling to the hiding Imam and the Ismailis to come out of concealment. If this version certainly embodies grain of truth, it implies that the Ismailis of Rudhbar were not yet acquainted with the whereabouts of the Imam. According to "Tarikh-i Guzida" (1st vol., p. 583), "They retained Alamut for almost one year before they were dislodged by a force sent against them by Halagu's son and successor Abaqa (d. 680/1282)." It is also related that the Ismaili dais of Rudhbar had communicated a report to some unknown dais, and the latter had transmitted it onwards till it reached to the Imam. Shamsuddin Muhammad is reported to have instructed his Iranian followers to observe taqiyaand adjust themselves in pursuant of the conditions of their localities. Henceforward, the Iranian Ismailis came to know of Shamsuddin Muhammad as their Imam.
Virtually, nothing else is known about the activities of Shamsuddin Muhammad in northern Azerbaijan. Certain allusions in the still unpublished "Safar-nama" of poet Nizari Kohistani indeed indicate that Shamsuddin Muhammad and possibly his successor lived in concealment in Azerbaijan, or southern Caucasus.