Really, this album and probably others by Dream Theater should rightfully be interpreted as a whole.
To me, the whole album is telling a story, and one can't really grasp the whole concept without looking at all of it. In pt1, a man has lost his faith, and rebukes the God figure. However, (correct me if I am wrong) it seems that his father, a holy man, dies and leaves him a quest to prevent the evil to take over the world. As the album progresses, he meets remnants of old sins, sees the atrocities of man, prophecies against war. Even either experiences or witnesses the attempted retribution of a soul. At the end, in pt2, he reaches his place, and the "circle" waits there for him. They claim he is a heretic, despite his efforts, and judge him. He turns a full 180, sells half his soul in order to destroy those who claimed to be holy, but sees his own error and turns from the darkness as well, and claims the power from the good entity and destroys those who are the true heretics.
Or maybe I'm full of it, I don't know, but either way one should look at the full album for the story to fall together.
Really, this album and probably others by Dream Theater should rightfully be interpreted as a whole. To me, the whole album is telling a story, and one can't really grasp the whole concept without looking at all of it. In pt1, a man has lost his faith, and rebukes the God figure. However, (correct me if I am wrong) it seems that his father, a holy man, dies and leaves him a quest to prevent the evil to take over the world. As the album progresses, he meets remnants of old sins, sees the atrocities of man, prophecies against war. Even either experiences or witnesses the attempted retribution of a soul. At the end, in pt2, he reaches his place, and the "circle" waits there for him. They claim he is a heretic, despite his efforts, and judge him. He turns a full 180, sells half his soul in order to destroy those who claimed to be holy, but sees his own error and turns from the darkness as well, and claims the power from the good entity and destroys those who are the true heretics. Or maybe I'm full of it, I don't know, but either way one should look at the full album for the story to fall together.