Nightjohn himself eventually becomes one of the largest symbols in the story. After gaining the knowledge and freedom that came with learning to read and write, he wanted to impart this to others. Though he is still present, it is only ephemeral, only at night in the pit schools where he serves as the "living embodiment of the will to learn, resist, and be free."
Perhaps another part of nightjohn that serves as a symbol is his body. Though it is covered in scars and mutilated, it represents in the fact that he is still living and passing on his knowledge the power of literacy and what it can add to the inside of a person, even if the outside is beaten and torn.