Clearly about the catholic church. All of the political interpretations are so off that I'm not sure the lyrics were actually read.

Guest wrote: Sinister means Left. Rouge means Red, which is a euphemism for Communist. This song is about Secular Humanism, typically associated with both Communism and Leftist politics, annihilating the religious establishment.

Interesting, I thought he was using the word rouge, as in, a cunning attempt to trick someone. I got that definition from the Clerks. Rock Lobs.

http://www.badreligion.com/albums/14/The_Empire_Strikes_First

At the bottom there is an audio clip of Greg explaining the meaning of the song .

This song chronicles the negative influence of Religion, particularly Christianity, on Western society from the Inquisition (no one expected THAT) all the way to the religious exploits of the modern day that hurt us all.

Sinister means Left. Rouge means Red, which is a euphemism for Communist.
This song is about Secular Humanism, typically associated with both Communism and Leftist politics, annihilating the religious establishment.

According to Greg Graffin, this song is about the catholic church: "Child molesters and Jesuits, holding secret conference..... and only God will ever know" talks about how most of the priests have been molesting the alter boys and in turn, preaching to everyone. I however detect a "hint" of sarcasm in "Only God will ever know!"

This song describes the Catholic church, aka Sinister Rouge (SR).
It reminds us that the Church was the former dominating force of Europe for a long time. And they were not a benevolent empire ("Innocents burned alive at the stake") and had crusades and corruption, etc. Then Europe and modern society in general rejected the church, "the modern world rejects your hand." But while their authority died, the institution remained, and the "seeds of ancient lies" took root. And waited.
So now, in the form of child molestation scandals, resentful SR is coming back to haunt society. The uncontrollable, inconsolable Sinister Rouge needs to even the score for his banishment to irrelevance in modern society. Like a desperate animal, SR exacts his revenge on the young and defenseless.

While I agree with the general interpretations of this song and its relation to the Catholic Church, the current state of American politics and foreign policy adds a different spin to it. To me, "Sinister Rouge" relates to the current Republican administration (the "red" party) governing its actions by a radical, evangelical Christian mentality (which often takes on the same spirit as the Spanish Inquisition).
The modern world is clearly rejecting America's evangelical right-wing agenda.

Sinister Rouge is the dark side of the cloth, so to speak, and this song is clearly about the pedophilia scandals that became a big news story last year.
The way I interpret this song, the Church had a stranglehold on European Society through the Dark Ages with "innocents burned alive at the stake", etc. Then the Enlightenment came along and the Church was relegated to the background, and its power has been kind of ceremonial for the last couple hundred of years or more ("centuries waned, authority died"). But its sinister side, its evil authoritarian and violent ways, did not disappear, they were only in hiding ("scattering seeds of ancient lies"). And like an organic creature, a rejected, defeated, and irrelevant organic one, the Church struck back with a sick vengeance via the pedophilia scandal. This was the Sinister Rouge coming back for more, punishing individuals but really a society that relegated it to the background.

This song deals with the archaic institution known as the Catholic church. The first two lines have already been covered. The second two comment on how, even though the church now holds no real power, they cling to the same outdated beliefs they always have.
The 2nd verse talks about the problems of the modern-day church, and the old senile pope who cannot see it. The last verse is basically saying that we have to learn from the mistakes they made.

The first verse was not about the witch burnings, it was about the inquisition ( nobody expects the Spanish Inquisition).
This song is not talking about the ' greed ' of the catholic powers. A lot of them got there from nothing and truly believe in it all.

My interpretation: For almost 500 years the Catholics ruled most of the civilized world and they were not too nice to people known as heretics. They subjected them to questioning, torture, even death. That's the first verse
The second verse fast forwards to modern day. Molestations, money corruption and such things.

This song talks about the dark side of religion, like the evils that have been involved with the catholic church.

This is about the frailties of the Catholic church through the ages. The first verse talks about the early days of witch burnings and how the structure for their misinformation started when the first priest read the Bible. The second verse is about the current-day molestations, and how even the authority doesn't even see the hidden picture. The chorus is how they will keep on going until their dying day (They are unmarried and celibate. What else would they do?). At least we have hope in that the third verse shows that we are ignoring their ways in our society.

This song is about nothing more than Christianity and the catholic church. It talks about how they sit back and basically conspire against everyone and everything. It isn't about religion to them; it's about greed and what they want.
It basically says humanity has been lead and deceived by them for centuries.