SpongeBob and Patrick arrive at the entrance of Jellyfish Fields ready to jellyfish. They slowly watch the Ranger go to open the gate to the Fields. They show him their jellyfishing licenses and take pride in doing it, to which he is not amused. SpongeBob then takes a moment to realize how lucky he and Patrick are to be among the jellyfish, and they take the time to pay tribute, and sing the Jellyfishing Song. Patrick then notices a large billboard and points it out to SpongeBob. They read the sign and find out that the Shelly Superhighway is going to be built over Jellyfish Fields, so SpongeBob goes into town alone, trying to stop the destruction of Jellyfish Fields.
No one listens, so SpongeBob goes to work, very sad. Mr. Krabs says he is actually supporting the construction of the highway, much to SpongeBob's dismay. He explains that he will get more customers if the highway is built. SpongeBob discovers that Plankton is the founder of this highway and that his plan was to build over the Krusty Krab to run them out of business. The ending of the highway leads to the Chum Bucket to steal all the customers that Mr. Krabs once had. Mr. Krabs storms over to the Chum Bucket where he orders Plankton to stop this highway. He then tells the two that he has already had everyone in town agree. It cuts to a flashback to a court where people are were told to say "I" if they support the construction of the highway. The people who agreed included Mr. Krabs, who humorously agreed only because he likes saying, "Aye!" Mr. Krabs remembers this in pity.
SpongeBob and Patrick then pass out flyers and sing Give Jellyfish Fields a Chance trying to get Bikini Bottom to save Jellyfish Fields. They find out that people are on the highway's side when they are pelted with their own flyers. Nat then tells SpongeBob and Patrick that the highway is what everyone wants by crushing the sitar that SpongeBob was playing as part of the song. The police then come and control the riot, arresting SpongeBob and Patrick because SpongeBob didn't have a license on his sitar (actually resisting the highway project) even though SpongeBob claims his grandma gave him the sitar and it didn't come with a license. The police then throw them out in the middle of nowhere (or edge, Patrick corrects SpongeBob). During this time, Patrick remembers what his Great-uncle Cletus said before he was arrested in a Freedom March and urges them to continue to support Jellyfish Fields. After they are abandoned, they think a parade would get people to go down with the Highway, but as soon as they are brainstorming (literally), a parade for the highway passes by, followed by Plankton, with a Paver, to build the highway. SpongeBob tries to stop him, only to be crushed by the Paver while Patrick plays the trumpet. All the life is sucked out of Jellyfish Fields as well, causing all of the jellyfish to retreat.
The scene then cuts to a severely polluted and trashed Bikini Bottom with the Shelly Superhighway forming a concrete arch over the Krusty Krab. SpongeBob, Squidward, and Mr. Krabs are in the Krusty Krab, which is out of business like Plankton planned. Mr. Krabs says that he will initiate "Plan Z-niner niner" which causes SpongeBob to break down and Squidward to ask what it is. Mr. Krabs says he will give the formula to Plankton and close The Krusty Krab. Squidward is delighted that he no longer has to work at the Krusty Krab. However, the Jellyfish soon attack Bikini Bottom, causing the Bikini Bottomites to panic. Just as Mr. Krabs is about to sell the formula to Plankton, Mr. Krabs flees while Plankton is grabbed and stung by the jellyfish. SpongeBob uses this chance to convince the Bikini Bottomites to restore Jellyfish Fields through a news broadcast. Everyone still replies no until SpongeBob asks if they were kidding, to which they reply yes. Soon SpongeBob rides Plankton's paver in an attempt to demolish the highway, but it does not budge. A severely stung, but still standing Plankton appears and gloats that his highway is indestructible. However, the Bikini Bottomites help SpongeBob by pushing the paver, giving them enough momentum to unpave the highway and restore Jellyfish Fields. Panicked, Plankton tries to stop it but is crushed by the paver. The Krusty Krab is back in business and the episode ends with the Bikini Bottomites in Jellyfish Fields singing The Jellyfishing Song.
SpongeBob's Last Stand had an online game featured on SpongeBob.com, which also helped Nickelodeon's The Big Help (an organization/movement about people playing on an online game, who would do events/things to save the environment and biodiversity in real life, in order to get points in their game; also, the Big Help was promoted by various Nickelodeon stars, like Miranda Cosgrove, among others).
The Krusty Krab sign is different, now stating, "over 2,478,921,437 served," as a parody of the McDonald's sign, which says, "Billions and billions served."
This episode is famous to environmental protesters since it features environmental protesting, which was SpongeBob and Patrick protesting against the construction of Shelly Superhighway which threatened Jellyfish Fields.
It is revealed Plankton has been stealing Mr. Krabs' mail for the past five years.
The parade includes flower girls, a marching band, a float with clowns and models, a fish with long legs, conjoined twins, a Santa fish on a limo, old folks being whipped by the wrestlers from "Krusty Krushers," a bagpipe band, a giant cat float, a choir, rock stars, and Plankton in a bulldozer.
A season four episode of Rugrats had an episode with a similar title called "Angelica's Last Stand."
"Plan Zed-99" (Niner niner as Mr. Krabs pronounces it) means surrender the formula to Plankton. Zed is the pronunciation of letter Z in some countries, the last letter of the alphabet, and when it comes to two-digit numbers, 99 is the very last number.
In the first scene with Ben Flenny, he uses shoes, but in the second, when Bill appears, the reporter is not wearing shoes.
Plankton breaks the fourth wall when he says "Observe in this conveniently timed flashback."
The title card is popping up through the Shelly Superhighway.
On the highway supports around the Krusty Krab is a range of different writing and drawings. One is a drawing of Squidward.
After the highway goes over the Krusty Krab and goes over a loop, it goes into the Chum Bucket, but that's impossible because the Chum Bucket is across the street to the Krusty Krab.
The episode's title, "SpongeBob's Last Stand," is a reference to "Custer's Last Stand" (also called the "Battle of the Little Bighorn"), a battle during the Great Sioux War of 1876-77, in which the Lakota and Northern Cheyenne Native American tribes completely defeated the 7th Calvary Regiment of the United States Army.
The line "Frankly, my dear sponge, I don't give a barnacle." is a parody of a famous line from Gone with the Wind.
When Plankton says "I love the smell of tar in the morning," it parodies the famous line, "I love the smell of napalm in the morning.," from the film Apocalypse Now.
The Shelly Superhighway plan is also a reference to Robert Moses' plans for the Long Island Transportation System.
The line "And stop calling me Eugene" is a possible reference to the quote "and don't call me shirley" from the film Airplane!
In the final scene before the camera zooms out, if one can pause it at the right moment, one will notice that some of the characters eyes are slightly off.
Before Mr. Krabs says that he likes saying 'I', the fish next to him is yellow, but when he says it, the fish is green.
Right before the commercial break, the rainwater is spreading, but afterward become a circular puddle.
At the beginning, when SpongeBob and Patrick are catching jellyfish, Patrick says he caught a "five spotted jellyfish" but really it had only one spot.
However, due to Patrick's immense stupidity, he probably can't even tell the difference between five spots and one spot, so this may not be an error at all.
Oddly, after Plankton built the highway, all other streets in Bikini Bottom disappeared. It's possible that this was done purposely to make Plankton's highway the definitive street of Bikini Bottom.
Patrick played the trumpet with his left hand, when he is actually right-handed.