Scenario 1: Keeping in tone with the core message of family.

First act: Sandy and B.O.O.T.S. (Bureau of Official Texas Science) are set up to have a good connection. Sandy and her blood relatives are also revealed to be on bad terms on account of Sandy abandoning them for science. But she is on excellent terms with the town of Bikini Bottom on the simple fact that they are friends and neighbors of hers. We also see her and Sparky share at least one scene bounding over a mutual interest. As well as set up that Abigail and Brendon (I think that is their names) have a lovely dynamic. Abigail is the smart cookie who has an encyclopedic knowledge of everything but suffers from crippling self-doubt. Brendon is honestly just chilling most of the time but has a knack for engineering.

We cut to the villain of the movie, Sue Nami, and set her up as a corporate antagonist, simply wanting to generate as much profit as possible. She buys B.O.O.T.S. and starts investing resources into making Bikini Bottom effectively a theme park with its residents as attractions. (Like the original Space Jam, now that I think about it.) Abigail and Brendon try to object but are easily bribed with free snacks. (Sue can be characterized as someone who only really cares about others in transactional terms to contrast Sandy who has loyalty and love because she is just a genuinely good girl.)

Second act: Sandy catches wind that B.O.O.T.S. has its entire stated purpose overhauled because of Sandy's research. (Which she manages to figure out on her own because she is brighter than the average squirrel.) She then tries and fails to protect Bikini Bottom. But manages to save at least Her faithful companion Sparky, as well as SpongeBob, Patrick, and Squidward. They go after the ship that took them and quickly clock that the B.O.O.T.S.O.T.S. plans to put Bikini Bottom right on top of where Sandy's blood family settled down. We can have a scene where, at first, it seems like Sandy's blood family and her friend's family will not be able to get along long enough to save Bikini Bottom and its inhabitants. But luckily, it is short lived as the two groups find unlikely common ground. Her family can forgive Sandy for leaving, and the two groups resolve to band together.

Cut to the villain, who is furious that not only does Bikini Bottom not have some of the star players but also catches wind that Abigail and Brendon are plotting to sabotage her plan. She sends them to capture Sandy and all her fish folk friends to kneecap any plans they might have had, hopefully. Unfortunately for her, Abigail and Brendon's loyalty is to Sandy, no matter how many snacks they are fed.

Third act: Our heroes are now a united force of Sandy and all her allies and manage B.O.O.T. B.O.O.T.S. by deceiving Sue into believing they had given up, but it was all a deception! For, as soon as they get a hold of the town's holding bubble, they make a hasty escape to leave the facility. Sue stops them and starts monologuing about how betrayed she feels by Abigail and Brendon. Abigail and Brendon are quick to shut her down, pointing out that she only had their loyalty because she bought it. SpongeBob is quick to shut her up when he threatens to report her directly to Neptune for the crime of kidnapping an entire town. She lets our heroes have their win, but now she is so far in debt she must get a minimum-wage job to scrape by.

Sandy learns the all-important message of family is who you choose.

The End.

Scenario 2: Villain Redemption

Act 1: Set up Sandy and SpongeBob's relationship specifically, highlighting how much the two need each other. Establish how the town relies on them both to help solve problems. Establishing Sandy's employment with B.B.O.O.T. catches wind of Sue Nami, and her pitch for Sea Pals at B.B.O.O.T. realizes that Sue is using Sandy's research for her product.

Sandy attempts to shut down the entire project. Instead, Sue compromises with Sandy and promises to take only one resident of Bikini Bottom. Sandy found this request reasonable enough and agreed.

The project is green-lit, and the next day, SpongeBob SquarePants, Gary, and the Pineapple house are taken away.

Act 2: Sandy takes it upon herself to go after Sue, but Mr. Krabs, Patrick, and, surprisingly, Squidward all volunteer to go with Sandy. They get to Texas and bump into Sandy's family. (This is just a fun aside and doesn't affect the main plot except to set up just how much SpongeBob means to his friends.)

Cut to SpongeBob meeting Sue. Sue is ecstatic to meet him, but SpongeBob is less than pleased to meet her on account of the kidnapping of him. However, Sue then explains herself. She's always wanted to hold a fish but never got a chance because they would die in her hands. Now, she has her unique scientific formula to change SpongeBob's D.N.A.D.N.A. to give him the power to breathe air and become immortal. But also make copies of him so no child could ever be heartbroken by a dead, dried-out fish again. SpongeBob then must turn her very gently down on the latter but offers her a chance to hold him close. He can explain how, due to his friend Bubbles (or because he is an absorbent Sponge if, for whatever reason, cross-movie continuity is out of the question), he can survive outside of water longer than most fish.

Act 3: We see the group of SpongeBob's friends charge in at an odd sight. SpongeBob is being held close by a very content Sue. Sue lets SpongeBob go, turns to his friends, and apologizes for making such a mess. She then helps SpongeBob and the rescue party back to Bikini Bottom. When she is then punished for her crimes by Neptune, who sentences her to a life of servitude under him, she is transformed into a mermaid, and we cut to a year later, which shows Sue visibly happier as a mermaid as friends surround her.

The End.

Scenario 3: A surprise Jimmy Neutron SpongeBob SquarePants crossover event.

(So, to be honest, this is just me indulging in my NickToons Unite hyper fixation, but it could work potentially.)

Act 1: Set up both Sandy and Jimmy are working for B.O.O.T.S. that they are aware of each other's work, Sandy's research is fueling Jimmy's inventing. Establish that Sandy loves Bikini Bottom but is still homesick in Texas. Establish how sick of Texas Jimmy is and how he would really like to see Bikini Bottom-up close like Sandy but can't because of his work.

Jimmy sits in on the Sea Pals Project pitch by Sue and tries to shut it down but can't convince them against it. Jimmy attempts to warn Sandy, but it's too late, and now the two must work together to save Bikini Bottom.

Act 2: Jimmy uses his portal to instantly transport Sandy to Retroville so the two of them can start brainstorming ideas. However, Sandy noticed that she had grown quite a bit larger than her friends. Jimmy must explain that his portal temporally put her to scale with humans. More to the point, they come up with a plan to break Bikini Bottom from B.O.O.O.T.S. Two separate plans, Jimmy and Sandy are having trouble getting along because, for one, Jimmy has an ego as big as his hair. For another, Sandy's plans amount to her kicking Sue's butt, as she is just too angry to make any sneaky plans. Cut to Sue, who is boasting about outsmarting two geniuses and revealing her greed in trying to sell Bikini Bottom fish folk. SpongeBob is intimidating. Then, off-screen, Jimmy and Sandy's plan fell apart spectacularly. They were dragged by security to Sue in less than good condition. They're locked up in a big cage.

Act 3: SpongeBob takes a moment to listen to Jimmy and Sandy's shared distress and grievances about getting in each other's way. SpongeBob then gave them both a pep talk. He gives Sandy a little boost by reminding her of all the incredible things that she's already carried out. He tries his best to lift Jimmy's spirits, but he doesn't know that much about Jimmy. (This can be set sometime before the events of Unite. Alternatively is set after Unite, in which SpongeBob is only able to pull from that knowledge specifically.) Either way, the two smarty pants try one more time to work together and manage to succeed at rescuing Bikini Bottom by sending it through Jimmy's portal. Sue is punished by getting fired because she disrupted an entire ecosystem for profit.

Jimmy now visits Bikini Bottom regularly, and Sandy can go home anytime. All thanks to portals! Also, maybe a moral of pride and true teamwork.

The End