At Halagu's request, Ruknuddin sent his representatives with the Mongol envoys to all the castles in Rudhbar, instructing for their destruction. Some forty castles were thus demolished. Halagu proceeded to the foot of Alamut, whose Ismaili commander was Muqadinuddin. Leaving Balaghai behind to besiege Alamut with a large force, Halagu then set out for Lamasar. After a few days, the garrison of Alamut dismounted. Berthold Spuler writes in 'The Muslim World' (London, 1969, 2nd vol., p. 18) that, 'The fortress Alamut offered a desperate resistance to the onslaughts of the Central Asian hordes and only succumbed after a prolong siege.' Towards the end of Zilkada, 654/December, 1256, all the persons in Alamut came down with all their goods and belongings and after three days, the Mongols climbed up to the castle and seized whatever those people had been unable to carry off. They also plundered freely whatever they found in the castle, and then set fire to its building and its library. Meanwhile, Ata Malik Juvaini, who had accompanied Halagu to the foot of Lamasar, had been granted permission to inspect the library. He saved a number of choice books, including some Ismaili works, as well as certain astronomical instruments, before consigning the library to flames. Thus, the accumulated literary treasure of about two centuries was consumed to ashes. Juvaini himself writes, 'I burnt them all' (basukh tam). Edward G. Browne termed it, 'world's renowned library.' Arif Tamir writes in 'Khams Rasail Ismailiyya' (Beirut, 1956, p. 195) that, 'The Mongol destroyed the Ismaili library containing one and one half million volumes.'
As for the Alamut, Juvaini writes, 'It was a castle whereof the entries and exits, the ascents and approaches had been so strengthened by plastered walls and lead-covered ramparts that when it was being demolished, it was as though the iron struck its head on a stone, and it had nothing in its hand and yet resisted. And in the cavities of these rocks they had constructed several long, wide and tall gallaries and deep tanks, dispensing with the use of stone and mortar....And from the river, they had brought a conduit to the foot of the castle and from thence a conduit was cut in the rock half way round the castle and ocean-like tanks, also of rock, constructed beneath so that the water would be stored in them by its own impetus and was continually flowing on. Most of these stores of liquids and solids, which they had been laying down from the time of Hasan-i Sabbah, that is over a period of more than 170 years, showed no sign of destruction, and this they regarded as a result of Hasan's sanctity. (2nd vol., pp. 720-1) Juvaini goes on to tell how a large body of Mongol soldiers were employed in demolishing the castle: 'Picks were of no use: they set fire to the buildings and then broke them up, and this occupied them for a long time.' (Ibid.)

Meanwhile, at Lamasar, Halagu had failed to induce the surrender despite the services of Ruknuddin as intercessor. He left Dayir Buqa to beleaguer it with an army, but it did not surrender until 1258. He quitted Rudhbar on 13th Zilhaja, 655/January 4, 1257 and reached his encampment at Hamdan. On 22nd Zilhaja/January 13, Ruknuddin's family and servants were billeted in Qazwin, but he himself accompanied Halagu. From here, on Halagu's request, Ruknuddin sent his emissaries to the Ismaili castles in Syria, instructing them to guard the castels as subjects of Halagu until such time as he himself should arrive there.

On 18th Shawal/November 8, Halagu encamped on the hilltop opposite Maimundiz. The Mongol armies began to prepare for a siege. The Ismaili forces gained initial victories and rained down stones from their own mangonels upon the besiegers. The Ismaili warriors using the mangonels, were made with a pole of hard wood raised in a slanting position, supported by a strut at a point a quarter of its height from the top, and fixed in the ground at some distance from the main pole so as to support it. At the top of the pole was the emplacement for the axle to which the shaft was attached.
On the second day of fighting, the Mongols brought into a play a Chinese ballista with a range of 2,500 paces. The garrisons of Maimundiz now ceased fighting and asked for truce, which was granted. Meanwhile, on 25th Shawal/November 15, the Mongols resumed their bombardment on Maimundiz on large scale. The Ismailis strained every nerve to meet the situation and the danger hovering on their door, but they found themselves utterly helpless in the face of these nomadic hordes that poured down into the Ismaili territories like ants and locusts. At length, Ruknuddin asked for a yarligh, granting him self-conduct. He first sent down his son and another brother Iranshah with a delegation of nobles and on Sunday, the 29th Shawal, 654/November 19, 1256, he himself dismounted from the castle, embosomed with a group of dignitaries including Nasiruddin Tusi, Khwaja Asiluddin Zuzani and the vizir Muayyaduddin. He was however well received by Halagu.

One of the first acts of Ruknuddin's reign was to send an envoy to Yasa'ur Noyan, the Mongol commander camping at Hamdan (the ancient Ecbatana, the Arabs Hamadhan). Yasa'ur replied in this context that Ruknuddin should present himself in person before Halagu, whose arrival was now imminent. This was the first of a long series of messages exchanged in 654/1256 between the Ismailis and the Mongols.
In Zilhaja, 653/January, 1256, Halagu crossed the Oxus and passed the winter in the meadow's of Shafurqan to the west of Balkh. The Russian orientalist Wilhelm Barthold has computed the army of Halagu at about 129,000 men and a thousand Chinese artificers, who were skilled in the construction of military machines and in preparing and using every species of inflamable substances for attacking walled towns and fortified strongholds. Halagu entered Iran through Khorasan in Rabi I, 654/April, 1256 and conquered Tun and proceeded towards Tus. During the Mongol operations, the Ismailis are said to have occupied about 360 mountain castles and strongholds.

In Jamada I, 654/May, 1256, Ruknuddin Khurshah had sent his brother, Shahanshah with a delegation to announce his submission to the Mongols. They met Yasa'ur near Qazwin, and Ruknuddin delegated his own son to accompany the Ismaili mission thence to Halagu. Nine days later, Yasa'ur not only detained Shahanshah, but also invaded the Rudhbar without any reason to demonstrate Mongol's power and attacked the Ismaili forces on a mountain top behind Alamut, but he was forced to withdraw after a short while. He then vacated the whole region upon instructions from Halagu, who had now received Ruknuddin's embassy at Quchan. Halagu professed his satisfaction with Alamut's embassy and his own ambassadors reached Ruknuddin at the end of Jamada II/July and delivered a decree, full of encouragement and benevolence, insisting to demolish his castle and come in person. Ruknuddin did in fact destroy some castles. He also demolished the gates coated with lead and removed the battlements and turrets of Alamut, Lamasar and Maimundiz. The Mongol ambassadors, accompanied by Ruknuddin's envoy Sadruddin returned to report the situation to Halagu. Ruknuddin is said to have asked a year's grace before presenting himself. In the beginning of Shaban/September, the Mongol envoy came with a new proposal that the Ismaili Imam should immediately present before Halagu, and in his absence a Mongol, named Tukel Bahadur would act as a caretaker governor in Rudhbar. Ruknuddin sent his reply through an embassy led by his vizir, Shamsuddin Gilaki and Saifuddin Sultan Malik, who accompanied the Mongol ambassador and reached Halagu on 17th Shaban/September 9, asking for a year's grace and exemption of Alamut and Lamasar from the demolition order, but the Mongol demonstrated their impatience.

Halagu now set out from his encampment near Bastam to launch his assault on the Ismaili strongholds in Rudhbar. The main Mongol force proceeded from different directions. The right wing of Halagu forces led by Buqa Taymur and Koke-Ilgei advanced by way of Mazandaran. The left wing under the Chaghatai prince Teguder and Ket-Buqa proceeded through Simnan and Khuvar. While Halagu himself with the principal army, followed parallel route leading through Firozkuh, Damavand and Ray. He alighted at Damavand for a while and sent yet another message to Ruknuddin. The Imam was asked to come at once to Damavand, and were he to be delayed upto five days by his preparations, he was to send his son in advance. Ruknuddin dispatched his son on 17th Ramdan/October 8. Halagu returned the boy and suggested that if Ruknuddin could not come till later, he should send another brother to relieve Shahanshah. On 5th Shawal/October 26, Ruknuddin sent out his brother Shiranshah with 300 men, who arrived at Halagu's camp two days later.

Meanwhile, the vizir Shamsuddin Gilaki had returned from Girdkuh and brought its governor, the Qadi Tajuddin Mardanshah, before Halagu, while Girdkuh still held out. Shahanshah was relieved and sent back to Rudhbar with the message that if Ruknuddin demolished the castle of Maimundiz and presented himself in a person before Halagu, he would be received with honour and and given immunity. By this time, the Mongol armies entered Rudhbar from all sides. Halagu set out from his base at Piskildara on 10th Shawal/October 31 and advanced towards Rudhbar through Taliqan.

The Ismailis continued to retain good relation with the Abbasids and Khwarazamshah. Alauddin Khwarazmshah (d. 617/1220) and Jalaluddin Khwarazamshah (d. 628/1231) were very proud of their wealth and grandeur and their relations with the Abbasids and the Ismailis became deteriorated and fell into a swift decline. The Mongol routed the empire of Khwarazmshah in 628/1231 with no difficulty, because no Muslim power came to help them. It must be noted that the kingdom of Khwarazmshahis was founded by Anushtagin (1077-1097). This dynasty ruled for 153 years from 471/1079 to 628/1231 and produced 8 rulers belonging to seven generations.

Hence, only two big powers remained in existence in Islamic world, i.e., the Abbasids and the Alamut.

According to 'Jamiut Tawarikh' (p. 122), the construction of the fortress of Maimundiz began in 490/1097, but Kashani (d. 738/1338) determines in 497/1103 in his 'Zubdat al-Tawarikh' (p. 144). Juvaini (2nd vol., p. 627) however writes that it had been built in the time of Alauddin Muhammad. It seems that the location had been selected earlier, where a small fortress was built, known as Maimundiz. In the time of Alauddin Muhammad, the site had been freshly chosen and projected for a stronghold. His officers and ministers had surveyed the heights and summits of the mountains during 12 years until they chose a lofty peak, and built there a castle, and provided it with ample supply of water.
The site of Maimundiz, located to the north of presently village of Shams Kilaya and westward from Alamut. Because of the great altitude, the cold was so extreme as to make it impossible for beasts to find a home or live in that location from the beginning of autumn until the middle of spring. The family of Alauddin Muhammad and his attendants were shifted from Alamut to Maimundiz.

The site of Maimundiz was identified in 1960 by an expeditionary party organised at Oxford University for exploring the Ismaili castles of northern Iran, vide 'The Castles of the Assassins' (London, 1963) by Peter Willey. Dr. M. Sutude in 'Qila-i Ismailiyya' (Tehran, 1966, pp. 108-122), who is well grounded with the geographical area, rejected the identification of Maimundiz made by Peter Willey's expedition.

Shamsuddin bin Ahmad al-Tayyibi (592-652/1195-1254) was an eminent Ismaili poet in Syria. He travelled excessively in Iran and visited Alamut during the period of Alauddin Muhammad, where he served as a court-poet. His poetical works are not accessible. He left Alamut most probably after the death of Alauddin Muhammad, and returned to Syria, where he died.

Alauddin Muhammad's rule was long and prosperous. It was a period of both intellectual and political activity. The glory of his rule was the patronage of science and learning, attracted a bulk of scholars from outside. He was fond of shepherding and used to visit the villages to help the people in their dairy products, and the cattle breedings. His old enemies conspired through his close advisor, Hasan Mazandaran, who killed the Imam on 29th Shawal, 653/December 1, 1255. His body was found at midnight in a wooden hut, near his sheep-fold in the village of Shirkuh in the western part of the district of Alamut. Alauddin Muhammad had many son's whose detail is not accessible. It is however known from Juvaini that Shahanshah, Shiranshah and Iranshah were his sons, and the elder one was Ruknuddin Khurshah, who was consigned the office of Imamate.

Soon afterwards, Guyuk dispatched Eligidei to Iran at the head of reinforcements for the Mongol armies already stationing there, with instructions to assume supreme command in reducing the Muslim holds, beginning with Alamut. Guyuk intended to follow after, but his death prevented the operations, which was charged some six years later, to his nephew and successor Mongke (1251-1259), who appointed his brother Halagu (1256-1265) to command an army to Iran, Iraq and Egypt according to the resolution of the Mongol National Assembly (quriltai) held in 649/1251. Halagu did not reach Iran before the beginning of 654/1256, but had dispatched an advance army of 12,000 men from Mongolia in 650/1252 in command of Ket-Buqa to join with the Mongol garrison already camping in Iran. Ket-Buqa crossed the Oxus in 651/1253 and soon afterwards, attacked the Ismaili strongholds in Kohistan. His troops drove off the cattle of the people of Tun, Turshiz and Zir-kuh and slaughtered and pillaged throughout that region. The towns of Tun and Turshiz were however captured, but the Ismailis recovered Tun very soon. Ket-Buqa also reached at the foot of Girdkuh with 5,000 men, where he constructed elaborate siegeworks, digging a trench around the castle, and erecting a wall around the trench. The men then formed a ring behind that wall, and a second wall and a trench were constructed around the men, so that they were apparently left secure in the middle with no possibility of attack from either side.
Leaving his officer, Buri with the charge of siege at Girdkuh, Ket-Buqa proceeded to attack the castle of Mihrin, near Girdkuh and Shahdiz. In Shawal, 651/December, 1253, the Ismaili garrison of Girdkuh made a valiant nocturnal assault on the Mongols, killing a hundred of them, including Buri. The siege however continued and in the interim, the disease of cholera broke out in the summer of 652/1254. It was reported to Alamut that most of the garrisons were perishing and the castle was on the verge of falling. Alauddin Muhammad immediately supplied reinforcements, including his three officers at the head of 110 men, each carrying a load of two maunds of henna (Latin Lawsonia inermis, Arabic hinna, the shrub) and three maunds of salt. The garrison's stock of salt had been exhausted, and as for the henna, we are told by the author of 'Jamiut Tawarikh', himself a physician, that there had not been prescribed in the books of medicine that henna was a drug against cholera. The people of Girdkuh had an experience however that once water being scarce, some of them had drunk that henna water and were cured. It was for this reason that they had asked for henna from Alamut. The 110 men forced their way through the ranks of the besiegers, suffering only a single causalty; one of them fell into the trench and dislocated his leg; his comrades lifted him on to their shoulders and carried him into the castle. The garrison, thus restored to its full strength, and continued its resistance until 659/1270.

Halagu was yet in Samarkand and was about to cross Oxus on the eve of the death of Alauddin Muhammad, who, according to Peter Brent, might have been strong enough to resist for a long time against the Mongols, vide 'The Mongol Empire' (London, 1976, p. 135)

After this rebuff by the West, the Ismailis made their final approach to the Mongol's court. In summer of 643/1246, on the enthronment of Guyuk (1246-1248), the next new Mongol's chief; Alauddin Muhammad, along with the Abbasid caliph al-Mustasim (640-656/1242-1258) and many other Muslim rulers, sent a mission in the Khangai mountains in Central Mongolia. The Ismaili ambassadors, Shihabuddin and Shamsuddin, the former governors of Kohistan delivered a memorandum to Guyuk. Neither they nor the Abbasid ambassador were well received, and on that juncture, the Mongol demonstrated a negative attitude towards the Muslim rules.

The pact between Imam Jalaluddin Hasan and the Mongols, as hinted by Juvaini and explicitly described by Rashiduddin, became impaired afterwards. In 635/1238, Alauddin Muhammad dispatched an embassy, in cooperation with the Abbasid caliph al-Mustansir (d. 640/1242) to Louis IX (d. 1270), the king of France, and Henry III (d. 1272), the king of England, to report the incoming stormy inroads of the Mongols, and to evaluate possibility of an alliance with the Christian West against the Mongols. Mathew Paris (d. 1259) has written in his 'Chronica Majora' (ed. by Henry R. Luard, London, 1876, 3rd vol., pp. 487-9) the account of this embassy in England. The Bishop of Winchester, who was present at the audience, interrupted the envoy's appeal with harsh words, reflecting the hostile policy of the church against the Muslims.

Nasiruddin Tusi was born in Tus, Khorasan in 597/1202. In his youth, about in 624/1227, he entered the service of Nasiruddin Abdu Rahman bin Abu Mansur (d. 655/1257), the Ismaili governor in Kohistan. During his long stay at Qain and other strongholds in Kohistan, Nasiruddin Tusi procured his close friendship with the Ismaili governor, to whom he also dedicated in 633/1235 his famous work on ethics, entitled 'Akhlaq-i Nasiri'. He went to Alamut and espoused Ismaili faith. In his 'Sayr wa Suluk' (pp. 38-42), he narrates how, after his initial dissatisfaction with scholastic theology and philosophy, he came to realize the necessity of following an infallible Imam who would guide reason to its perfection. In all probability, Nasiruddin Tusi willingly embraced Ismailism during the time of Imam Alauddin Muhammad. According to Farhad Daftary in his 'The Ismailis: their History and Doctrines' (London, 1990, p. 408), 'There is no evidence suggesting that these outside scholars were detained in the community against their will or that they were forced to embrace Ismailism during their stay amongst the Nizaris.' He enjoyed the patronage of Alauddin Muhammad and his successor, until the collapse of the Alamut rule in 654/1256. The Mongol chief Halagu made him his trusted advisor, and built a great observatory for him at Maragha in Azerbaijan. He was a most voluminous writer too, and died in 672/1274. His 'Rawdatu't-Taslim' and other short treatises bear an Ismaili imprint. Seyyed Hossein Nasr writes in 'Science and Civilization in Islam' (Mass., 1968, p. 322) that, 'The universality of Nasir al-Din's genius, which some have quite erroneously taken for lack of principles, is shown by the fact that, while in the service of the Ismailis, he was able to master their doctrines and even wrote several works which contain some of the clearest expositions of Ismailism. Among these, the 'Rawdat al-taslim' is particularly notable, as a simple exposition of the basic doctrines of this important branch of Islam.'

The arrival of Shamsuddin Hasan at Kohistan marked with the outbreak of new conflicts between the Ismailis and their Sistan neighbours. Yaminuddin Bahram Shah bin Taj al-Din Harb (610-618/1213-1221), the local Nasrid chief of Sistan, had previously waged two wars against Alamut during the time of Imam Jalaluddin Hasan; and his nephew had sold the fortress of Shahanshah near the town of Nih to Alamut. Yaminuddin demanded from the Ismailis of Kohistan to give up the claim of the fortress, and threatened to capture it by force. Before the invasion of Yaminuddin on Kohistan, the four fidais had killed him on 5th Rabi II, 618/May 29, 1221 at Zarang.
It was followed immediately by the succession issue in Sistan among the sons of Yaminuddin. The Ismailis of Kohistan supported Ruknuddin against his younger brother Nusratuddin, whom the notables placed on the throne. Like his father, Nusratuddin continued his claim on the fortress of Shahanshah. Soon afterwards, Ruknuddin gained the throne of Sistan with the help of the Ismailis in 619/1222. In the meantime, the Mongols invaded Sistan without staying there, and Ruknuddin had also been killed by his slave. The notables of Sistan put on the throne Shihabuddin bin Harb and his brother Ali, to the dissatisfaction of the Ismailis, who again had their own candidate, Uthman Shah bin Nasiruddin Uthman. They acquired support from Khwarazmian commander, called Tajuddin Yinaltagin, who was then stationed at Kirman, for the rights of Uthman. Yinaltagin arrived in 622/1225 at Sistan with his troops, and defeated the forces of Sistan. Instead of placing Uthman on the throne, Yinaltagin retained this power with him for almost a decade.

Thus, Shamsuddin, the Ismaili governor of Kohistan commanded his forces in a battle against Yinaltagin, and inflicted a defeat to him in 623/1226. It was after this battle against Yinaltagin, who deputed Minhaj Siraj Juzjani as his envoy to conduct diplomatic negotiations with the Ismailis of Kohistan. Minhaj Siraj concluded a truce with Shamsuddin at Nih on behalf of Yinaltagin, and as a result, the Ismailis pursued an independent policy in its local affairs, and developed important trade route with other regions, which were the source of acceleration of their economical conditions. When Minhaj Siraj returned to Sistan after negotiations, Yinaltagin forced him to go once again to Kohistan to declare a war against the Ismailis, but he did not consent to set out on a second journey, as he had determined upon undertaking a journey into India. This refusal did not meet with the approval of Yinaltagin and he commanded to detain him for 43 days in the fort of Safhad of Sistan and prohibited his going beyond the walls.

In the meantime, Alamut gave refuge to Ozbeg's son, Malik Khamush, and to Jalaluddin's brother Ghiasuddin, who were dismissed from their posts by the Khwarazmshah in 625/1228. The Ismailis helped Ghiasuddin despite the Khawarazmian blockade of Rudhbar, but he was there murdered.

In 625/1228, while the Ismaili envoy Badruddin was travelling east across the Oxus to Mongol court, Jalaluddin Khwarazmshah ordered at once to stop all the caravans in that direction, pretending that a Mongol envoy was on his way to Syria in the company of some Ismailis. In compliance, his vizir Sharaf al-Mulk put to death in Azerbaijan a westward Syrian Ismaili caravan of seventy merchants. Hence, Alamut sent an emissary to the Khwarazmshah, demanding successfully retrieval of the goods taken from the murdered Syrian Ismailis. In the meantime, Ghiasuddin took flight from Alamut which had enraged Jalaluddin Khwarazmshah.