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As Jerry marvels at the frequent nudity of his girlfriend, Melissa, George hears that Jason Hanke is making amends as part of his Alcoholics Anonymous program. Recalling that Jason once insulted him, George is convinced that he's in line for an apology. However, while Jason takes the time to apologize to Jerry, he doesn't do anything similar for George. Meanwhile, as Elaine is insulted by a fellow employee's efforts not to be exposed to her germs, Jerry teaches Kramer how to save time in the shower.
When approached about an apology, Jason's sarcasm only makes George look foolish. So George now feels he's owed two apologies. However, his complaints to Jason's Alcoholics Anonymous sponsor only get him invited to a recovery group for those with uncontrollable rage. Concluding that seeing her unclothed all the time is too much to bear, Jerry then decides to use his own nudity to give Melissa a taste of what he's been experiencing. But the demonstration backfires and drives Melissa away. Meanwhile, Elaine is ostracized by her colleagues over her treatment of Peggy.
Having decided to do everything in the shower from now on, Kramer calls on Elaine's boyfriend David for help installing a garbage disposal. When Elaine complains about how things backfired, David reveals that he also used to be very afraid of germs just like Peggy. However, his efforts to intervene only cause a relapse of David's own fears. Meanwhile, when they try to resume a fully-clothed relationship, Jerry can only think about how great she looks naked, while Melissa is repulsed by her own memories of him nude. Finally, when an offer to apologize doesn't satisfy him, George's complaints cost Jason both his sanity and his new job.
Several previously unknown facts emerge during "The Apology": Kramer's garbage disposal is manufactured by Clarkman; Puddy has been a recovering germaphobe for the past ten years; and George reveals that his uncle was an alcoholic.
We learn in this episode that Jerry knows how to make a radish rose: "Insert a knife into the center and twist; then to make it bloom, soak it water for thirty to forty minutes."
According to Elaine, the problem with Jerry's body is that he has chicken wing shoulder blades. Elaine has previously said that she and Jerry broke up because they had problems with their physical chemistry.
In this episode, we see that Puddy sometimes sits at home and stares at the walls. He also does this on the flight with Elaine in "The Butter Shave."
"So she coughed."
"Coughing, naked, It's a turnoff, man."
"Everything goes with naked."
"When you cough, there are thousands of unseen muscles that suddenly spring into action. It's like watching that fat guy catch a cannonball in his stomach in slow motion."