It is understandable that this situation is upsetting to you. Try not to take the song literally. Young children often express themselves through symbolic play, and music is one such expression. Instead of trying to stop the behavior at night, try to find out about it during the day. You can start by asking your son to tell you a story about a little boy whose parents have left him. Young children aren't as verbal as older kids, so you may want to have him play the story out with his toys.
Keep in mind that you want to find out about the meaning of the song to your son, not the reality of the situation. You've written that you spend all your spare time with your son and don't know why he's singing this song. Maybe your son has a grandparent who is getting old or a friend who recently switched schools and is saying something to ward off his anxiety about these changes. Perhaps your son has just learned about death (if a beloved pet has died, for instance), and is playing around with this notion through his song.
Another possibility is that the song is actually a response to how present you and your husband are in your son's life. Is he going to school soon? Perhaps your son is mastering the fear of losing you both by saying the worst. Sometimes people say the worst to feel less afraid.
While you explore the meaning of your son's song to him, offer continued reassurance and love. As you begin to uncover its meaning, you can even talk with your son about including additional verses that incorporate this new understanding.