In short Ismaili prominence was ended by Saladin in the West (although internal politics had weakened the Fatimids significantly by his rise) and the Mongols in the East. I've written about Saladin's relationship with the Shia population under his control here: https://www.reddit.com/r/AskHistorians/comments/mjgiub/how_did_saladin_treat_shiite_muslim_communities/gtaxxl0?utm_medium=android_app&utm_source=share&context=3,

In brief he dismantled their networks for propagating Ismaili belief and replaced them with Sunni, usually Shafi'i institutions, as well as destroying their books on jurisprudence and history.

The most famous division within the Fatimid Caliphate is the Musta'li Nizari schism. In which al-Mustansir's designated successor Nizar was passed over in favour of his younger brother Abul Qasim Ahmad who took the reginal name al-Musta'li (The high/ the superior) upon his ascension. This was the work of al-Afdal Shahanshah who became the ruler of Fatimid Caliphate in everything but name as the 20 year old had not been groomed to rule in the same way his brother had. This led to a rebellion in December of 1094 trying to establish Nizar as Caliph which was put down and Nizar was executed by immurement (left in a room with no access to food or water). One other famous prisoner taken was Hassan-i Sabbah who would later escape (there are a series of entertaining but probably apocryphal tellings of how) and establish the Nizari Ismaili State in Iran and Syria. Better known as the Assassins or Hashashin they would continue to harass and be harassed by the Fatimids for the remainder of the  Fatimid Caliph Imams. This included the killing of several important figures within the Fatimid Caliphate including  al-Afdal Shahanshah and Fatimid Caliph al-Amir bi-Ahkam Allah.

On top of the internal problems of power hungry viziers, a fractured Ismaili population and a rebellion, al-Musta'li was also facing external threats like the Seljuk turks and the First Crusade. He did manage to recapture Jerusalem from the Seljuks before the Crusaders took it from him less than a year later. By the time of the third Crusade Saladin had come to power. With Fatimids gone the Assassins continued until around 1256 CE. The Mongols invaded in 1253 but the two had been interacting since the early 1220s. There's some controversy about its veracity but the general story is that the Assassins were plotting to kill Mongke Khan and upon finding out about the plot Genghis ordered the complete destruction of Ismailism. "None of that people should be spared, not even the babe in its cradle" However things seemed to cool down until Mongke became Great Khan, where he instructed Hulugu to destroy the Nizari and the Abbasids.

Alamut, the most famous of the Nizari fortressess fell in 1256. Upon its surrender it was plundered and Ata-Malik Juvayni a Persian historian who had been accompanying the Mongols saved a few Qur'ans and some scientific equipment before burning everything related to Ismailism to try to stamp out their "heresy and error" he also claims to have read and then burned Hassan-i Sabbah's biography. He contradicts himself somewhat in regards to what happened to the Ismailis captured from claiming that they were all executed to claiming any boy taller than the axel of an ox cart was executed and the women and children enslaved. To quote Juvayni in reference to the Nizari Imam “He and his followers were kicked to a pulp and then put to the sword; and of him and his stock no trace was left, and he and his kindred became but a tale on men’s lips and a tradition in the world.” There are issues with this telling: 1. Alamut wasn't the last fortress to fall, 2. There were Ismailis outside Persia and 3. The Imams son wasn't killed and briefly took control of what remained of Alamut in 1275.

Girdkuh was the final fortress in Persia to fall, after a 17 year siege the fortress had run out of cloth for clothing and the Mongols had begun constructing a permanent town around the fortress. After their surrender the besieged were all executed.

With that the Ismailis in the East were forced underground outwardly posing as Sufi mystics, Twelvers or Sunnis.

After the Mongol invasions the only place the Ismailis had a degree of autonomy was Mamluk ruled Syria as a semi autonomous community until 1273, before being fully subdued around 1277.

With that Ismailism was forced completely underground until the end of the concealment period was announced by 46th Nizari Imam and 1st Aga Khan Hasan Ali Shah.

Sources:

Beben, Daniel. (2017). Remembering Saladin: The Crusades and the Politics of Heresy in Persian Historiography. Journal of the Royal Asiatic Society. 28. 1-23

ʿAta Malik Juvayni, The History of the World Conqueror, translated by John A. Boyle (Manchester, 1958), pp. 16–17

Walker, Paul, Exploring an Islamic Empire: Fatimid History and its Sources, (London, 2002).

Daftary, Farhad, The Isma'ilis Their History and Doctrines, Cambridge: Cambridge University Press, 1990.

Virani, Shafique, The Ismailis in the Middle Ages A History of Survival, a Search for Salvation, Oxford Scholarship Online, May 2007, Print ISBN-13: 9780195311730