A Sudden Realization
They were certain that the smell of non-threatening and threatening objects had been taught to differentiate Kyle, which is why they were confused as to why he was acting as such. But then, there was something they realized, which is when suddenly everything clicked!
An Orchestrated Crime Scene
Smith was the first who put two and two together. Kyle, he remembered, had just wanted to see John. There were signs of loneliness in his recent actions, and his best friend and former partner were absent. He knew that after his police actions, John was going to run.