“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!”
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, the Flanders family is not so lucky; Ned's house is the only one that has been totally destroyed.
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 condradicts the other stuff) but gets no answer.
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, the toilet's in the kitchen and the door to the main bedroom is only large enough to accommodate a cat at best. The makeshift house soon crumbles, and Ned, who knows that everyone tried their best, tries containing his anger, but his temper explodes. He angrily speaks his mind about everyone's efforts, then rants on about specific residents, such as Bart and Krusty, ending his tirade by calling Homer "the worst human being I have ever met." Homer states, "Hey, I got off pretty easy."
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. There, he is treated by 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 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.
Dr. Foster, now having seen that his earlier therapy was inappropriate, enlists Homer to help Ned learn to appropriately express his emotions, as Homer is the person who Flanders harbors the most resentful feelings towards, as Homer does the same towards Flanders. 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 getting worked up over what he hates about the post office, then casually saying he hates his parents; suddenly, he feels like a weight has been lifted from his shoulders.
Shortly thereafter, Ned is released from Calmwood, and tells everyone 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." Everything then returns to normal and Ned winks.