John Cooper finally actually explained the meaning of this song in a concert at Pittsburgh that I went to. Here's exactly what he said: "A young girl and a young guy who were in a situation and found out she was pregnant. It was hard because they were young, they weren't married, they didn't have any money, and they were scared to death. They didn't know what to do. The only option they thought they had was to terminate the pregnancy. They went to a clinic, and had the procedure done, went home, and for a moment they felt a little bit better about their situation, they thought all their problems had gone away, but eventually something happened that they didn't expect: an intense sadness and guilt and pain. They went to a therapist, and her suggestion was to treat it like there was a loss in the family. So they did three things: 1. Held a funeral for the baby. 2. Gave it a gravestone. 3. Named her Lucy.