Lyric discussion by Muse-sick Mann 

For what it's worth, if there ever was a Mary, Gary has successfully kept her a secret for over 30 years.

So, if there was no Mary, then there's no tragic love story behind this song, and it's just the result of a gifted songwriter creating and preserving an air of mystery around one of his most popular songs.

The lyrics are sufficiently vague to be relatable to a broad audience, both male and female, and even has an adequate religion flavor, so much so that it's even sung by church choirs. Bravo, Gary! That's the way to make a song broadly appealing, and to keep audiences intrigued for decades.

So, if there was no Mary, does that mean Mary's Prayer has no meaning? Of course not! What follows is my interpretation, which I doubt Gary will ever refute, because an artist interpreting his own work tends to dwindle its appeal, and he's far to clever to do that. However, I'm gonna take a stab at it.

The titular Mary isn't a reference to the Blessed Virgin, despite the additional references to the similarly titles popular penance prayer(more on that later). Mary is a former girlfriend, and one he didn't adequately appreciate, when he still had the opportunity. Mary was devoted to him, but he took her for granted. So, if Mary was such a great chick, why not go get her back, instead of just writing her a defeatist love song? Because, Mary is no more....metaphorically "washed away."

The song begins from Mary's perspective, from her "wonderful," "Heavenly" home. Mary is now perfected, not only in the singer's memory, but in a genuinely angelic state, from which she serves as the singer's guardian angel, sending him daily blessings

In the next verse, we hear the singer's lament, not only for the Earthly loss of Mary, but also for his own shabby behavior, when she was still corporeal. That things ended badly, and he never had a chance to repent and reconcile fills him with guilt, as though she might still be earthbound, if he'd behaved in a more worthy manner.

The tree metaphor is a reference to the singer's attempt at stardom, to climb the charts, and "reach the top." He doubts his ability to make it without divine intervention, and suggests that his guardian angel, Mary, can "blow [him] up there,” or carry him the rest of the way, if he isn't able to make it on his own.

The Hail Marys are obviously penance for his feelings of guilt. He's asking his Mary if she'll wait for him("leave a light on in Heaven for me"), if he'll perform this act of contrition. He hopes to reunite with her in Heaven.

So, what about the Millionaire? My guess is that he through that in to soften the song, to provide an alternate interpretation, to broaden its appeal among his female audience, and to round out the religious subtext; in the last interpretation, she would become the bride of the Son whose "Father's House has many Mansions."

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