"Prayer to God" is a legendarily ugly song. Almost overly so. But what helps elevate it from an unlistenably hateful screed delivered from a lesser band to something that is going to make it a cult hit for decades to come is the dark humor/debased social storytelling from industry troll/anti-charismatic frontman Steve Albini. Lyrically, the song's protagonist starts out almost humbly, addressing his prayer "to the one true God above," followed by an admission that he realizes he hasn't prayed in a long time. And sure, God is likely busy with other prayers, but clearly something has come up that is of sufficient importance to warrant the breaking of years and years of spiritual silence. "There are two people here, and I want you to kill them."
The first of these two people, "Her," is an ex-lover. The protagonist describes scenes of domestic intimacy: the fastening of necklaces, the closing or garments in getting dressed (suggesting time spent together, undressed), and--just so the listener is aware that this woman isn't simply some desired specimen, perhaps observed from afar--a spot on the base of her neck where he used to lay his face. Three quick scenes of a shared, physical relationship. If God likes, he can just strike her in that place once, killing her quickly. The idea of the "mercifully quick death" is perverse. "Her" has clearly engaged in something that the protagonist views as justifiable for death. But because he "loves" her, he will do her the "favor" of making it quick. In fact, as he thinks about it, he enjoys the poetic nature of having God strike her there. That's where it should be done.
Him," on the other hand...
And of course there's a "Him." What else would warrant the God-assisted murder of an ex-lover? The protagonist could give a shit about Him and whether or not he suffers in his demise. The protagonist's attitude noticeably changes. Where he was talking about Her, the thoughts--even murderous thoughts--were tied to scenes of putting on jewelry delivered almost gently, over the comparatively bare-bones guitar-only bed of music. Him gets the full band, complete with the thuggish pounding drums of Todd Trainer. The protagonist also lets his first "fucking-as-interjection" slip. The thought of Him raises the protagonist's blood. So much so that after professing to not care if it hurts when Him dies, he decides that in fact, yes....he does care....Him should definitely hurt when he dies. He should "cry like a woman" first (a bit of misogyny there, inserted by Albini to help flesh out while Her decided to seek solace with Him in the first place). He wants Him to be killed in a way that, after he's cried, gives him hope that somebody may come, and then God can dash those hopes and fucking kill Him. Fucking kill Him. Fucking kill Him. Repeat over and over, getting louder and more deranged as the idea and bloodlust and desperation and impotency (because why ask God to do it, otherwise) racks the protagonist.
As a final note, when the protagonist says "there are two people here...," the word "here" suggests that these two people are in the room. The protagonist has perhaps captured them, and is now hoping for divine intervention to do his dirty work in a scene that gets more and more terrifying and fucked up the longer one dwells on it. Which, for a two and a half minute song, is quite a lyrical feat.