I'm sorry, for everything that I've done
But when I call you never seem to be home
I think that she is telling him not to be mad at her. I think that "you never seem to be home" represents how he doesn't feel like he wants to give her a second chance or forgive her. All she wants to do is apologize, but he's locked her out.
mirror, my sword and shield
My missionaries in a foreign field
For some reason I can't explain
I know Saint Peter won't call my
This person is hearing all of these wonderful sounds, but he knows he cannot be a part in them. He has to be strong for the battle, whether it is emotional or physical. This person is asking the listener to be what he needs.