It's about a heartbroken boy looking for love, but not finding it. He soon realizes that nobody loves him as much as God does, and decides to find it within himself to believe in something greater than himself. "He's calling your name" is the call to grace, and the realization that he is a sinner, and only through his faith in Jesus's death and resurrection to nullify his sins, can he be saved from the power of sin and death. "My shame you took with those nails in your hands" is obviously a direct reference to Jesus's crucifixion for mankind's sins, and the Holy Ghost is mentioned, saying he will be faithful. Gotta love the lyrics.