In midst of a quiet afternoon, the wind starts to pick up, which leads Lisa to find out that a hurricane is on the way. Lisa warns Homer, but he is skeptical since there is not any record of a hurricane ever hitting Springfield. Lisa reminds her father that the records only go back to 1978, "when the Hall of Records was mysteriously blown away". The evening news confirms that "Hurricane Barbara" is close, resulting in panicked citizens storming the Kwik-E-Mart and Homer attempting to secure the Simpson home. The hurricane strikes and after a few treacherous hours, the storm ends and the family cautiously leaves the basement. Initially, they are thankful to see that their home is untouched and Marge comments that everything works out if one has a little faith.
Meanwhile, next door Ned emerges from a heap of rubble and sees that his house was destroyed, along with everything else he owned except the family gravestones, while all the houses around his are intact. Ned is relieved that his family escaped serious injury, but it turns out to be little solace since he does not have home insurance, as he considers insurance a form of gambling. The Flanders family is forced to move into the Rescue Center in the church basement, although they appear to be the only family to be affected to that extent. Ned is further discouraged after learning that his business, the Leftorium, was looted following the hurricane. Distraught with annoyance, Ned begins to believe that God is punishing him and, seeking answers, he goes to read the Bible in the church but receives a paper cut. Interpreting it as further punishment, he sits down and laments that he is falling apart, even after doing everything the Bible says, "even the stuff that contradicts the other stuff."
The following day, Marge arrives at the church and takes the Flanders family back to their house, completely rebuilt by the people of Springfield. Overjoyed, Ned inspects the house, but becomes increasingly dismayed as he discovers its extremely shoddy construction. Immediately after the inspection, the house collapses. Ned tries to calm down, knowing that the townspeople tried their best, but is unable to contain his rage and finally snaps, lashing out at all the residents of Springfield, and directing his most vehement invective at Homer (who believes he got off easy). Ned then drives himself to Calmwood Mental Hospital to seek psychotherapy.
While in the asylum, Ned is visited by his childhood psychiatrist, Dr. Foster, who tells Ned about his childhood life - as a completely out-of-control brat raised by beatnik parents who did not believe in discipline. As a result, the young Ned went through the University of Minnesota Spankalogical Protocol, which involved eight months of continuous spanking. The treatment worked so well that it rendered him unable to express any anger at all, and all Ned's repressed anger built up inside him until he erupted.
Dr. Foster enlists Homer to help Ned learn how to appropriately express emotions, as he is the person who Flanders harbors the most resentful feelings towards. After several failed scripted insults, Homer manages to get Ned to open up about some of his repressed dislikes, finally admitting he hates his parents, after which he immediately feels better. Upon hearing this, Dr. Foster declares Flanders cured and he is immediately released. Outside the hospital, Ned is greeted by the townsfolk of Springfield including the rest of the Simpsons and his family, who cheer him. Ned promises that from now on, if anyone does something he does not like, they will hear about it, which Dr. Foster tells him is very healthy. Ned then adds, "And if you really tick me off, I'm gonna run you down with my car." Homer responds by laughing and saying, "Ned, you so cra-zay!" as he and Ned begin to laugh, before the end credits begin with a crazy clockwork version of The Simpsons theme.