Aaron was granted leave from the exploration, but he couldn't travel alone back to Rock City, especially with what was happening around. Lots of things changed while Aaron was inside the ruins,
The cults increased their attacking intensity. No one has any idea why that was so. No one has time to investigate that either. They were busy fighting off the cultists.
All of a sudden, the cultist attacks increased in number. They were not reduced to a number as the previous intelligence suggested.
When the Supreme was imprisoned, the alliance had a chance to actively attack the assets of the cults, rather than passively defending.
In times of war, there would be times when Offence is the Best Defence.
The alliance, with the information they obtained from the Supreme, did the same. They actively hunted the cult holdouts.
It was understood that either the cults would be wiped out or they would burrow deep underground for a while before resurfacing.