This song is obviously about Leonard Hoenberger and his wife Pearl whom he refers to as his "Pearl of the Stars" in the novel "Year of the Black Rainbow".

"Each night I wish to God he’d let her rest
This hurts me more than any man can bear
She’s my angel from the west
There will never be one to take her place"
(Pearl was captured and is being tortured by Mayo Definwolf as a way to get Leonard to help him construct a virus. It hurts Leonard because the construction would mean the end of everything basically. There will never be one to take her place because he loves her so much.)

"When you go I will know
Follow you to the stars"
(He'll know when she dies and he will kill himself.)

"And when the world burns apart
There’ll be a place for your car
I’d give you everything
If only I’d have known you’d take it
But you don’t, ‘cause you’re you"
(This part I am not so sure of... Pearl and Leonard's son Joseph were killed by Mayo Definwolf which caused Pearl to retreat into a shell where she needs no support she can handle every thing herself. She doesn't want Leonard sympathy because she blames him for thier son's death.)

"And that’s why I’ll always love you
My pearl of the stars"
(Obviously, Leonard is in love with Pearl and he could never find someone he loves as much as he did her.)

"The pill she takes
The pain of which she drowns"
[Pearl is depressed (hence the pills and pain) because of her dead son and betrayal of her husband who created a virus and gave it to Mayo Definwolf to save Pearl.]

"Our baby sleeps next door
She’s new in town
I’ll tell her how wonderful you were
I’ll remember everything you were to me"
(Leonard created a baby (much like Coheed, Cambria, and Inferno) with thier genetics and she (Josephine the baby) is still growing in the tank.)

CHORUS