I read a song review about "Bad Moon Rising" and they said it was for Nixon and all the problems with the Vietnam War. I think the earthquakes and lightning describe the battle in Vietnam as someone said before.
And the part of "trouble on the way" and "bad time today" refers to the political weather in those years.
and "I know the end is coming soon" "Hope you got your thing together, hope you are quite prepared to die" "One eye is taken for an eye" was probably a prophecy dedicated to R. Nixon.

Mexican Fan