Songfacts®:

• Grant Lee Phillips once said that he originally intended the song to be about conspiracy theories concerning the assassination of John F. Kennedy, but he got a little carried away with the events of the Waco Siege and the song evolved. A lot of the lyrics can be interpreted as both:
  
  "They had him nailed up to a T with a T for Texas."
  - JFK was the first Roman Catholic US president. He was assassinated in Dallas, Texas.
  - David Koresh was believed by his followers to be the second coming of Christ, therefore being revered as the human embodiment of the Messiah.
  
  "His disciples with artillery they held the fort inside."
  - The "disciples with artillery" are JFK's secret service agents. Right after JFK was shot, one of them jumped onto the limousine and tried to regain control of the "fort inside."
  - Koresh's "disciples" firmly believed that Koresh was the second coming of Jesus Christ, and therefore believed that God was speaking through him. God wanted them to stay in the compound, so they stayed to defend the 'fort? with ample ammunition.
  
  "And by the time the story broke down at Dealey Plaza."
  - JFK was shot in Dealey Plaza in Dallas, Texas, where "our story broke."
  - The first message from Koresh is relayed over KRLD Radio in Dallas on February 28, 1993, the day the compound was first raided by the ATF.
  
  "We'd already covered the smoke, read the TV guide."
  - It seems that just as soon as these incidents occurred, the media had already broadcasted "smoke," or disasters, across the nation, on TVs, radios, newspapers, etc. So all one had to do was "read the TV guide." >>

  Suggestion credit:
  Lia - Beverly, MA