“Why me, Lord? Where have I gone wrong? I've always been nice to people. I don't drink or dance or swear. I've even kept Kosher just to be on the safe side. I've done everything the bible says, even the stuff that contradicts the other stuff. What more could I do? I feel like I'm coming apart here. I want to yell out, but I just can't dang-diddily-do-dang, do-dang-diddily-darn do it!”
After a hurricane blows through Springfield and destroys only Ned Flanders' home, Ned snaps after his friends and neighbors, including Homer did their best to rebuild his house when it was crudely re-built. He is checked into a psychiatric ward to discover the source of his sudden uncontrollable rage ever since his childhood.
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, or seemingly anyone elses. However, next door to the Simpson house, the Flanders family is not so lucky; Ned's house is the only one that has been totally destroyed as Ned and his family emerged from the rubble.
Ned is relieved that his family escaped serious injury, but that's of little solace since he does not have homeowner's insurance (having considered insurance "gambling"). The Flanders family is forced to move into the church basement. There, he watches news accounts of the storm's aftermath, and is further discouraged when footage is shown of the Leftorium, 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 after the hurricane, in an attempt to show their community spirit and friendship, Marge commissions everyone in Springfield to rebuild the Flanders' home as Marge takes Ned and his family to the newly-rebuilt Flanders' house as Homer gives Ned the tour of his new 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, the toilet's in the kitchen, and the door to the main bedroom is too small and it is only large enough to accommodate a cat at best and Homer and Ned leave the rebuilt Flanders' house as Marge responds to Ned what does he think about the new house. Unfortunately, the makeshift house soon crumbles, and Ned, who knows that everyone including Homer tried their best, tries containing his anger, but instead he is unable to contain his anger and as a result, his temper explodes. He angrily speaks his mind about everyone's efforts, then rants on about specific residents, such as Bart and Krusty. Ned voices out his opinion about Lisa being too cynical and forceful of others to accept her views when no one else cares for her opinions. She is offended and states Ned is the worst neighbor who doesn't appreciate his town's efforts, even if it's shoddy. Ned finally ends his tirade by calling his neighbor, Homer "the worst human being I have ever met." Homer then states, "Hey, I got off pretty easy." Ned then storms out and drives away as the townspeople of Springfield, including the Simpsons and his family except for Homer become shocked of what Ned has said to them.
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 for help. There, a nurse who is shocked he is there, calls his childhood psychiatrist, Dr. Foster, who reminds Ned that – because his beatnik parents did not believe in discipline – he was a rambunctious, out-of-control child in need of psychiatric counseling. That therapy, called the University of Minnesota Spankalogical Protocol, involved eight months of continuous spanking. There is a goof error, however, since Dr. Foster says that the therapy happened around "30 years ago", but since Ned is now 60, he should have been around 30 at the time. Although it reformed Ned from his bratty behavior, it worked so well that it rendered him unable to express any anger at all and resulted in his trademark nonsensical jabbering at moments when he was particularly close to losing his temper. This caused Ned to unknowingly repress his anger, until it built up inside him and erupted in his tirade of insults at the townspeople, including his neighbor, Homer.
Now having seen that his earlier therapy was inappropriate, Dr. Foster enlists Homer to help Ned learn to appropriately express his emotions, as Homer is the person who Flanders harbors the most resentful feelings towards and the feeling are mutual between the two. Homer arrives at Calmwood and Foster begins the therapy with several pre-written cards he wrote. After several flubbed tries Homer makes that results in failure and Ned retaining his nonsensical speech, a doctor assisting Foster suggests he try a new and unorthodox way to get Flanders to open up to his anger by letting Homer use his own approach. Dr. Foster is against testing it and wants to continue using his cards. The doctor convinces him to let Homer use his own approach when he noticed its failure. He believes that Flanders won't make any progress with the pre-written scripted cards Foster wrote unless they let him try it and help trigger the real source of Ned's anger. Homer takes this to heart and tries his own approach by claiming Ned is afraid to be human because humans hate things, but he likes everything. He disagrees and admits to Homer that he doesn't like everything. Ned mentions that he had been frustrated over the post office's lack of customer services all the time and ends it with admitting that he hates his beatnik parents for the lack of discipline he got from them over the years. Suddenly, he feels like a weight has been lifted from his shoulders and Dr. Foster eventually declares him cured.
Shortly thereafter, the newly-cured Ned is finally released from Calmwood and the townspeople of Springfield, including the rest of the Simpsons and his family greet him again, and Ned tells everyone, including Homer that he'll try harder at expressing his feelings and letting them know when he is upset, such as when he's really angry, "I'm gonna run you down with my car." as long as they will hear about it. Everything then returns to normal and Ned winks. Feeling a new sense of camaraderie with Ned, Homer calls him crazy and the men laugh.