Homer skips church one cold Sunday morning. After realizing the freedom and happiness he can obtain from having the house all to himself, Homer chooses to stop going to church altogether despite Marge's disapproval.
On a very cold Sunday morning in a blizzard, Marge is gathering the family to go to church, but Homer refuses and goes back to his warm bed. After sleeping extra-late, he finally gets up and has fun with the house all to himself: He cranks up the heat, dances in his underwear, makes his Patented Space-Age Out of this World Moon Waffles, wins a radio trivia contest, watches a boring debate on TV get preempted for what turns out to be an action-packed football game, and finds a penny under the couch. Meanwhile Marge, the kids, and the rest of the congregation shiver their way through the service and a rambling sermon, only to find themselves trapped at the end because the door is frozen shut. To make matters worse, Marge is unable to start the car due to the cold.
They finally get home, and Homer tells Marge he's had the best day of his life, all thanks to skipping church. Marge is very angry with Homer for giving up on his faith. Homer gives her his reasons (e.g. "What if we picked the wrong religion? Every week we're just making God madder and madder."), which does not please Marge at all. Later that evening, Marge prays for God to talk with Homer. Homer, meanwhile, falls asleep and has a dream where God appears to him. God is initially angry with Homer; once He has calmed, Homer asks Him what's the big deal of going to church when he's not a bad person and that he can worship in his own way ("I work hard and I love my kids... so why should I spend half my Sunday hearing about how I'm going to hell?") God sees Homer's point and agrees, ending the dream.
Marge, Reverend Lovejoy, and the Flanders family all try to win Homer back to Christianity and fail. The next Sunday morning, Homer is once again at home while everyone else is at church. He smokes a cigar while reading Playdude Magazines. Homer eventually falls asleep, and the lighted cigar he was smoking at the time falls on one of the magazines; the hot ash ignites the paper, and it isn't long before the house is engulfed in flames.
Homer wakes up to find the house in flames, panics and succumbs to the thick smoke. Apu, a Hindu, spots the blaze and takes up his duties as part of Springfield's volunteer fire department (of which the Jewish Krusty the Clown is also a member). Meanwhile, the Christian Ned tries to rescue Homer. After the fire department has extinguished the blaze, Homer fears that God was showing vengeance, but Reverend Lovejoy points out that God was actually working in the hearts of Homer's friends, despite their different faiths. Lovejoy convinces Homer to give church another try. Homer is at church next Sunday, but sleeps through the service. God appears in his dreams again and consoles Homer on the failure of his religion.