Civil War is from a concert in Japan. It is a protest song about war, that amongst other things says that a civil war only "feeds the rich while it buries the poor." It is mostly thought of as a tribute to 1960s anti-Vietnam War protest songs.
The song also mentions John F. Kennedy's assassination with the lyrics: "and in my first memories they shot Kennedy," as well as the battle for civil rights and the Vietnam War.
The song samples Strother Martin's speech in Cool Hand Luke ("What we've got here is... failure to communicate. Some men you just can't reach. So you get what we had here last week, which is the way he wants it... well, he gets it. I don't like it any more than you men.") and a Peruvian militant general's speech ("We practice selective annihilation of mayors and government officials, for example, to create a vacuum, then we fill that vacuum. As popular war advances, peace is closer").
The song ends with the telling line, "What's so civil about war anyway?", a word play on the dual meaning of the word civil.