While the battle against the Abyssal Army and the Agarthians intensified, Eligor was able to deal the killing blow to the Founding King of Agartha due to Nyarlathotep's earlier screech.
The Awakened Kings and Queens were only able to fight due to the Will that they had left behind in their bodies before they died.
Simply put, the Kings and Queens no longer had souls. They were more like programmed robots who were only ordered to do one thing.
So when Nyarlathotep attacked their minds, it caused a brief lag in their movements, creating an opportunity for their opponents to deal a fatal blow to their bodies.
The Founding King of the Ancient Kingdom, King Agarath, didn't die right away after getting stabbed in the chest by Eligor.