I found something on the tvtropes wmg section of Spongebob that might be a great way to close up the series if this was the plot to the sequel.
Warning this is a little bit of a tl;dr
"The Movie was not the end. When the show inevitably gets cancelled, there will be an episode in the future, right after the movie, where Krabs, happy at Plankton being neutralized as a threat and with a second Krusty Krab, will make more money than ever before. This will in turn result in him opening more Krusty Krabs, until he is the richest man in town. When he is the richest man in town, he will destroy all other businesses and bulldoze over people's houses for development, until everyone works for him, even the police, who use their batons to smack the shit out of anyone who resists. SpongeBob, who has been obedient up until this point, notices that the way people are living under Krabs is even worse than under Plankton, and realizes that Plankton was driven to commit his acts in the movie because of Krab's torture. He breaks him out of prison and forms a resistance group with him that also includes Sandy, with a lazer she designed and her Kung Fu for fighting, Patrick, with his same Robot that he had in "Sand Castles", and Squidward, who fights with god awful Clarinet music. They will assault the first Krusty Krab (which has become Mr. Krabs palace at that point), along with a mob of angry Bikini Bottomians, using things like musical instruments as weapons to fight Krabs' cops. Sandy detonates an explosive that creates a huge pit in the ground, and SpongeBob and Plankton confront Krabs on top of his palace. He fights them using a skull swordfish head as a sword (like in that one episode), where as SpongeBob uses his spatula as a sword and Plankton aids in the fight. Eventually, Plankton ends up on the ground with his limbs broken, and SpongeBob is hanging off of the building. Krabs prepares to strike him and let him fall to his death, but then someone shows up... Pearl. She is in tears at seeing what her dad has become, and grabs a bag of money, taunting Krabs with it. She then throws it over the ledge, and Krabs jumps over the grab it, leading to him falling down the pit. Outside, the police are defeated and Krabs is overthrown, and it is explained what happened to all the characters through the whole "text over a still picture accompanied by music" method. Plankton and SpongeBob use the recipe to open a new restaurant, which is moderately successful, and lets them make a living. Sandy become the cities new minister of science and Chief of Police. Squidward perfected his clarinet skills, and became a world famous composer. And Patrick is the president. Post credits, there is a clip of Krabs surviving the fall, crawling out onto the land, and noticing an odd looking fish. After talking to it, he grabs it, and gets swooped up into the air, because it was a fishing hook. Krabs is then cooked and eaten. Ok, so this would a little Darker and Edgier for a SpongeBob cartoon, but at least it would guarantee happy endings and get rid of Mr.Krabs."
http://tvtropes.org/pmwiki/pmwiki.php/WMG/SpongeBobSquarePants