The song was actually written about the play The Crucible which took place in salem during the witch trials Abigail was a girl who accused many innocent people of being witches thus causing them to be hung (no fair trial) and the man who cuts into the song is John Procotr (Abigail's former love interest) the reason he says "It's not on a ship we'll meet again Abigail But, in hell. I say God is dead" is because while in jail (he confessed to adultery witth Abigail), Abigail comes to him with some money pleading that he come with her on a ship in order to escape the noose in the morning but he refuses because he is disgusted by all the things she has done. The god is dead part came about because John realized that all these horrible things were happening and god wasnt intervening and then afterr fleeing from a salem crowd he ran into the middle of a lake and professed that god was dead, thus prompting his arrest as a heretic.