The frightfest begins in "Mr. and Mrs. Simpson" as Homer and Marge leave for what appears to be an ordinary day. But Homer is living a double life as a secret agent, and he is assigned to eliminate Kent Brockman. When a mysterious woman blocks Homer's shot and tries to kill Brockman herself, Homer finds that his competition "hits" a little too close to home. In "E.T. Go Home," Bart and Lisa come to the aid of Kodo the space alien, who's hiding from the government. Kodo asks them to help him obtain a long list of devices so he can reconnect with his home planet, but his intentions prove to be anything but friendly. In the final Halloween scare, "Heck House," Bart, Lisa and their friends spend Halloween night pulling pranks on unsuspecting people in Springfield. But when they go too far, Flanders decides he's going to spook them straight. Transforming the church into the "Heck House," Flanders is filled with supernatural power and subjects the children to his wrath of seven deadly sins.

Much to the Comic Book Guy's chagrin, Bart, Lisa and Milhouse check out a new comic book store called Coolsville, where they are treated like royalty by a friendly comic book buff named Milo (guest voice Jack Black). Coolsville attracts some real-life comic book creators, such as Alan Moore, Art Spiegelman and Dan Clowes (guest-voicing as themselves), and the Comic Book Guy wages war on Coolsville in an attempt to win back his customers. Meanwhile, Marge decides her middle-aged physique could use some help, and she launches a gym for "regular women." Marge's gym becomes wildly successful and as her fame grows, Homer fears she will dump him for a younger, more fit guy. Homer decides to take matters into his own hands to get into shape.