This song describes the operations of the FBI's "counterintelligence" program - which was to suppress any dissident movements in the '60s. Anyone from Malcolm X to Martin Luther King Jr. was silenced for speaking out against the government's injustices and illogic.
This song appeared in The Matrix at the very end of the movie.
Suggestion credit: Tim - Pittsburgh, PA, for above 2
The ending lyrics, "How long? Not long, cause what you reap, is what you sow" are taken from Martin Luther King Jr.'s speech "How Long, Not Long" in which King says, "How long? Not long, because you shall reap what you sow."