After forty days, Hulagu felt afraid of the outbreak of epidemics that might harm his army, because of the heaps of stinking dead bodies (more than one million that had not yet been buried). Consequently, he issued the following commands:

1- All the Tatarian army should leave Baghdad, in order not to be afflicted with epidemics, and move to another city North of Iraq, and a small Tatarian garrison should be left round Baghdad, since there was no threat in this region.
2- Real safety should be announced publicly in Baghdad: no Muslim should be killed randomly after those forty days. However, this safety was granted by the Tatars to give an opportunity for the Muslims to come out of their hiding places and bury their dead. It was a very difficult task and needed a long time to bury one million dead people; and unless it was accomplished quickly, assuredly, it would have a drastically negative effect on the atmosphere, not only of Baghdad, but also of all the cities of Iraq and Shaam, and the deadly epidemics would spread everywhere making no discrimination between Muslims and Tatars. For this reason, Hulagu wanted to get rid of those corpses with the help of the Muslims.
Actually, the Muslims who hid themselves in the trenches, graves and idle wells came out. But they came out with different appearances, weak bodies and pale color to the extent that they no longer recognized each other.
They came out and each one started to inspect the dead bodies and extract from the mounds of rotten corpses his child, brother, sister, father or mother.
What a great calamity!
The Muslims started to bury their dead. But, as Hulagu expected, the epidemics spread in Baghdad, and a great number of Muslims died because of the fatal diseases. As Ibn Katheer, May Allaah have mercy upon him, put it, "Whoever had been saved from being stabbed to death was caught by the plague!" It was a new catastrophe in Baghdad; and there is no strength and no power save in Allaah.
3- Hulagu commanded that Mu’ayyid Ad-Deen Al-‘Alqami, the Shiite, be the head of the ruling council of Baghdad appointed by the Tatars, on condition that he should be put under Tatarian guardianship.

https://en.islamstory.com/en/artical/20759/fears-epidemics