I read on vh1s storytellers that its about a childhood friend 'stephen'who had really back luck in life. A lot of his family died and he was kidnapped by his biological father. When he returned no one would mention it around him, whereas John would openly talk to him and ask him questions about it. They had a strong bond but they drifted apart till they met again at highschool or college. I think he wrote this song having not seen him for years and they eventually got in contact again. What a great song huh?