As I've pointed out a few times before already, the songs from Year of the Black Rainbow don't exactly follow the chronology of its respective novel. It's more accurate to say that the songs explore some of the events that occur within the novel, but the story really took a back seat on this album. But the album isn't so much about the physical confrontations going on so much as it is psychological and emotional. As many of the songs will later point out, the album has a love theme to it.

Which isn't all that surprising, considering Claudio's marriage to his long time girlfriend back in 2009. The songs from this album are peppered with her influence, some more obvious than others. "Here We Are Juggernaut" is a much more subtle reference, no doubt helped by the fact it's not quite a love ballad as seen on previous records. If you're not familiar with the term "juggernaut" allow me to divert your attention for a brief moment. A juggernaut, as defined by dictionary.com, "any large, overpowering, destructive force or object." For Claudio, the love between him and his wife is an overpowering force that can't be stopped. 

Conceptually, the song's title refers to a line that Coheed says to Cambria. This is an example of what I meant by the album not exactly following the chronology of the novel. Where "Guns of Summer" dealt with events leading up to their creation, I think "Here We Are Juggernaut" goes back to the mission the two are on. As IRO-Bots developed with superhuman abilities and powers, them and Inferno prove to be more than a match for most of the soldiers of Ryan's Red Army. Thus, they themselves are a juggernaut. Going back to the love theme, I believe the song is exploring the future relationship the two will have. During this part of the novel, it's evident that there's some mutual attraction between the two, despite Dr. Hohenberger's designs. However, Coheed and Cambria are "programmed" to believe any relationship they would pursue would prove disastrous.