I think the song is describing the Spanish Inquisition. Thousands of innocent people were executed by the Catholic Church, many families were devestated and torn apart. "Crowded streets are cleared away, one by one" describes once thriving populations dwindling due to persecution and prejudice. "Hollow heroes separate, as they run" describes "souless" Jews who resisted Queen Isabel, Archbishop Pedro Gonzales de Mendoza and Pope Sixtus iv's forced conversion efforts. "You're so cold but you feel alive, lay your hand on me one last time" could be describing an imprisoned "Crypto-Jew" who is awaiting torture and execution at the burning stake, speaking to his loved-one who had decided to bow to the Church and convert. The loved one is so cold because giving up one's culture is like losing one's internal flame. "Wise men wonder while strong men die" is describing the "Wise" leaders of the Church and the Monarchy, pondering the actions to be taken, causing strong-willed martyrs of Judaism to die. "Show me how it ends it's alright" describes the sentenced heretics' decision to remain faithful to their god and their beliefs. They are willing martyrs. "Show me how defenseless you really are, satisfied and empty inside, that's alright, let's give this another try" describes the Church's inability to snuff out the existence of the persecuted religions and their steadfast followers. The executors of the Inquisition are satisfied with their evil efforts, believing themselves in control of the people, yet the resistance will always give freedom of belief and expression another try.