The falling boulders created a dangerous, unpredictable environment that blocked everyone's view. Khan couldn't see the blue aliens and mutated Thilku anymore, and the same went for them.
That unpredictability worked in Khan's favor. He had attacked the ceiling to create that precise environment. He wanted chaos only he could read, and the rain gave him that.
'Flow,' Khan ordered to himself while inspecting the rain with the entirety of his senses.
The boulders fell with no specific pattern. Khan had to look at the ceiling to predict what would likely follow, but that ability had limits. His senses couldn't reach the layers of rocks that had yet to show their face, making their behavior impossible to study.
Nevertheless, the rain was different. Potential paths opened in Khan's view as he studied the falling boulders. He could use the large rocks to hide his figure and, hopefully, take the mutated Thilku by surprise again.