Homer thinks the hurricane is over, so he leaves the basement, but it's just the eye of the hurricane. The whole family tries pulling him back inside.
Homer lazily enjoys his latest mid-afternoon nap outside when the winds begin to pick up. Lisa consults her weather instruments and a question-and-answer book and finds out a hurricane will soon strike Springfield. Panicked residents quickly gather supplies and food at the Kwik-E-Mart, but Ned remains calm as the main storm approaches, having fitted his home with a large tent-like guard to keep it hunkered down. As the bad weather hits, and various hurricane-related gags play out throughout Springfield, the Simpsons do their best at family bonding in the basement. The storm finally passes, and everyone is overjoyed that the hurricane caused absolutely no damage to their home. Only the Flanders family, next door, has suffered. Their house, despite their precautions, is the only one to be destroyed.
Ned is relieved that his family has escaped serious injury, but, as he does not have homeowners insurance (having considered insurance "gambling"), the Flanders family is forced to move into the church basement. There, Ned watches news accounts of the storm's aftermath, and is further discouraged when footage is shown of his business, the Leftorium, being cleaned out by looters. Seeking answers from God, Maude and Rev. Lovejoy attempt to reassure Ned things will work out fine. He tries to find solace in the Bible, but all he gets is a paper cut. He tries asking God directly why he's being punished when he's done everything the Bible said (even the stuff that contradicts the other stuff) but gets no answer.
The next day, in an attempt to show their community spirit and friendship, Marge commissions everyone in Springfield to rebuild the Flanders' home. The job is completed in record time, and Ned is overjoyed—that is, until he inspects their workmanship, which turns out to be (at best) shoddy; for example, some of the floor is made of dirt, there's too much electricity in the living room, the toilet is in the kitchen, there are a lot of loose nails sticking out of the walls, there is a crack in the kids' bedroom with a scary clown poster that frightens Rod and Todd, and the door to the main bedroom is only large enough to accommodate a cat at best. Ned says that he has seen enough. After leaving the "rebuilt" Flanders home with Homer asking Ned of what does he think of the house that love built, the makeshift house soon crumbles, and Ned, who knows that everyone, including Homer, tried their (substandard) best, tries to calm down by containing his anger, but unfortunately, is unable to control his emotions and his temper explodes for the first time in anyone's recollection.
Ned angrily speaks his mind about everyone's efforts which shocks the entire crowd, then rants on about specific residents, such as Marge (for always overlooking the negative by staying annoyingly positive after she told Ned that they meant well and everyone tried their best to rebuild his house), Bart (for thinking he is so cool all the time and mocking his catchphrases at him after Bart stood up for Marge and told Ned to back off before Ned shocks the entire crowd again, to which Bart replies by becoming shocked and appalled), Lisa (as "Springfield's answer to a question no one asked" and for constantly butting in after she told Ned that Bart did nothing wrong), Chief Wiggum (for being a lousy cop after he laughed about Ned's insult at Homer's family), Krusty (for not being funny but Krusty ignores him as he is taking notes for his act), Lenny (for no reason as he does not know him but assumes he is a jerk; Lenny becomes confused and replies that he has only been here a few minutes and has no idea of what's going on), Moe (for being ugly and hate-filled; Moe replies to Ned by saying that he may be ugly and hate-filled, but then forgets the rest of what Ned said about him) and Milhouse (for always staring inappropriately after Ned passes by Milhouse and telling Ned, whenever they pass each other, that he [Milhouse] wears glasses too). Ned ends the tirade by calling Homer "the worst human being I have ever met!" Homer then states, "Hey, I got off pretty easy." Ned then angrily drives away, leaving everyone (except Homer, Chief Wiggum and Krusty) shocked and upset.
Fearing he has lost his mind and on the verge of a mental breakdown, Ned checks himself into the Calmwood Mental Hospital to seek therapy. A senior nurse recognizes his name and, panicked, calls Ned's childhood psychiatrist, Dr. Foster, who reminds Ned that – because his irresponsible beatnik parents, who are the polar opposite of their son in every imaginable way, did not believe in discipline – he was actually a rambunctious, out-of-control child, which Ned had completely forgotten following counseling. That therapy, called the University of Minnesota Spankalogical Protocol, involved eight months of continuous spanking. Although it reformed Ned from his bratty behavior, it caused his behavior to become extreme in the opposite direction, i.e. unable to express anger, which resulted in his trademark nonsensical jabbering at moments when he was particularly close to losing his temper. This caused Ned to repress his anger until it built up inside him and erupted in his tirade, which led to his returning to Calmwood.
Dr. Foster, now having seen that his earlier therapy did not work out, enlists Homer to help Ned learn to appropriately express his emotions, as Homer is the person towards whom Ned harbors particularly resentful feelings. After several flubbed tries with pre-written cards by the doctors, Homer tries his own approach by saying Ned is afraid to be human, because humans hate things but he likes everything. Ned denies this before going off on a tangent and getting worked up over what he hates about the post office. He then casually states that he hates his parents and suddenly feels like a weight has been lifted from his shoulders. Dr. Foster then declares Ned cured. Shortly thereafter, Ned is released from Calmwood. Springfield's townspeople (including the rest of the Simpsons and Ned's family), greet him and he tells them he is all better now and also lets them know he'll try harder at expressing his feelings, and, a tad too seriously, letting them know that when he is really angry, "I'm gonna run you down with my car". Everything then returns to normal and Homer tells Ned he's crazy and both laugh.