I have a question about the end of "The Crazies"?

I just saw the crazies and i have some questions :) well first how did everyone become crazy? i think its because of the contaminated water right? also how did david'sdeputy become crazy? if u know:) and at the end where it shows the plane-like scene what do they mean by saying "initiate containment protocol"? thanks if u can answer any of these questions <3