At the Krusty Krab, SpongeBob is making a Krabby Patty, and when he is finished, he cries as he gives it to Squidward so that he can give it to customer number five. The customer is revealed to be SpongeBob, who grabs the order, and eats it. Meanwhile, outside the Krusty Krab, Mr. Krabs calls SpongeBob into his "Hidey Hole" under the dumpster, where he keeps his belongings from when he was in the Navy in a treasure chest. They take it into Mr. Krabs's office, and Mr. Krabs tells SpongeBob about his old Navy buddies and his nickname "Armor Abs Krabs", and that his Navy Reunion is tonight. Krabs then tells SpongeBob to leave him to revel in his memories and get his work station in "shipshape", which he does with great enthusiasm. SpongeBob soon hears Mr. Krabs scream, and goes into his office, where he finds that Mr. Krabs has molted his shell, leaving him a flabby mess. He kicks his shell in frustration, causing it to fly into SpongeBob, who becomes stuck inside it. Mr. Krabs then tells SpongeBob to assume his identity at the reunion so that his Navy friends will not see him in this state.
At the reunion, SpongeBob initially puts on a convincing performance, but goes onstage to accept his "Trophy of Manly Toughness", he tells a story of him jellyfishing in Jellyfish Fields, and nearly reveals his true identity before Mr. Krabs tells him to get offstage. He attempts to leave, but Torpedo-belly insists that he body-slam him to test if he still has "armor abs". When he punches SpongeBob, he flies around the room, cracking the shell and revealing SpongeBob. They get angry, but the real Mr. Krabs emerges from the bush that he had been watching from and reveals himself. He begins to walk away in shame, until Muttonchop gives him back his trophy, saying that revealing his condition was the manliest thing anyone could ever do, and revealing that they have all been hiding something as well (Torpedo-Belly, for instance, had his torpedo removed). As Mr. Krabs walks away with SpongeBob, he says "Yeah, poor suckers. At least my shell will grow back!" and they both start laughing as the episode ends.
Mr. Krabs would again be seen without his shell in "Shell Shocked".
In June 2009, Time Warner Cable and Charter Communications labeled this episode along with Fear of a Krabby Patty as "SpongeBob Fun" which is supposed to be a shopping show, but as of April 2010, it has been corrected.
At the beginning when SpongeBob and Squidward are talking in their usual work positions, the Krusty Krab through the window alternates from the outer walls and windows seen through the window to simple yellow, orange, and black paint. This happens in a few other episodes.
This episode had the Nickelodeon productions light orange blob.
The epilogue cast has one of the working titles, "Molting."
This episode was originally titled "Molting" and then it was changed to "Shell Game", a reference to a pricing game of the same name on The Price Is Right, before finally being changed to "Shell of a Man", an expression meaning a man who is extremely depressed or disturbed by something.
Old Iron Eye's name is a parody to a character from the "Transformers" TV and Film series, Ironhide.
In the background on the wall you can see the same flags that were on the Krusty Krab. This is possibly a referance to it and where the flags on it came from.
SpongeBob was lighter then the shell because he went flying when Old Iron Eye and Torpedo Belly hit him.
SpongeBob is nearly as tall as Mr. Krabs' shell, but when Iron Eye punches him in the gut, he bounces around inside, making him appear very small in comparison to the shell.
The captions when SpongeBob says "Set course for full flavor!" instead say "That calls for full flavor!"