Lyric discussion by masterlessmaster 

Traditionally, a leper messiah was someone who was brave enough to preach to the lepers. Leprosy was feared greatly and lepers were ostracized and sent to live by themselves. Most priests feared these colonies and refused to have anything to do with them.

In context of these lyrics, the phrase takes on a slightly different meaning. Metallica, specifically, uses the phrase to refer priests and preachers who use religion to appeal to those who feel disenfranchised and alone. However, they don't use religion to make these people feel better, instead they guilt them into donating money. The term is not used with fondness in the lyrics. Most people see these fly by night preachers as little better than con artists.

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