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Before the events of re2, the government bought alot of BOW's and stuff from umbrella
^ William Birkin during his stay at umbrella tried to sell the government the G-virus, and the government wanted to do this so that instead of just buying from umbrella, they could develop their own and have a monopoly over it.
therefore after the approved bombing, they refused to really acknowledge their shady operations with umbrella. the nuking also was likely done to destroy any potential evidence that umbrella was dealing with the government.
basically, the government was in cahoots with umbrella.
"What is great in man is that he is a bridge and not an end"