This song is broken down into five sections:
Part I. Jesus Of Suburbia: This is an introduction of the character and tells about his home life.
Part II. City Of The Damned: This takes place in a 7/11 parking lot where he got into a fight and first realized he hated his friends and home: "The 7/11 where I was taught, the motto was a lie, it says home is where the heart is, but everyone's heart doesn't beat the same." The lyric, "At the end of another lost highway," refers to the group of kids who hang out under the highway where once again he doesn't fit in.
Part III. I Don't Care: This is where he becomes an outcast hating everyone and everything, and also in the story this is where St. Jimmy (a character Jesus created to heal the pain of a lost girlfriend) ties in, saying he hates everything now. This is where he considers leaving home.
Part IV. Dearly Beloved: Not much is known on this part. It's believed to be the peaceful, yet hard twilight between anger and happiness where you are content.
Part V. Tales From Another Broken Home: This is where Jesus just gives up and leaves. He doesn't know where he's going, but he's just going far away: "Running away from pain when you've been victimized." This is where he's leaving everyone that hated and hurt him, sort of starting over and beginning a new life.
Zach - Oklahoma City, OK, for above 2