NOTE: This spoiler was submitted by Jeremy.

The pirate Burger Beard (Antonio Banderas) is walking through a small island when he comes across a magic book held in the hands of a skeleton.
He swipes the book, and the skeleton comes to life. Burger Beard fights him until the skeleton punches him out of the island and back onto his ship. There, Burger Beard encounters a flock of seagulls, and he reads to them from the book.

The story takes place beneath the sea in Bikini Bottom, home of Spongebob Squarepants (Tom Kenny). Burger Beard notes how Spongebob loves everything and everyone he knows. He's working at The Krusty Krab when Mr. Krabs' (Clancy Brown) arch-nemesis Plankton (Mr. Lawrence) is plotting once again to steal the Krabby Patty secret formula. Plankton drops a huge jar of tartar sauce onto Spongebob and Mr. Krabs, forcing them to spring into action. With the help of his best friend Patrick Star (Bill Fagerbakke), Spongebob mans the battle station surrounding The Krusty Krab as Plankton attacks. Spongebob fires ketchup and mustard at Plankton's tank, and Patrick hurls a large jar of mayo at him, causing Plankton to crash. He then unleashes his giant robot to attack The Krusty Krab, only for him to run out of gas. Plankton emerges and admits defeat. He gives Mr. Krabs the last penny to his name and leaves to cry in shame. Mr. Krabs throws the penny in his vault.

Turns out the real Plankton was hiding in the penny while he sent a robot version as a decoy. Plankton comes before the secret formula and notices it's resting on a pressure plate. He opens the vault and finds a ship in a bottle. He removes the ship and leaves a piece of paper in there to make the switch. However, Spongebob enters the office and sees Plankton with the formula. Spongebob runs over to grab the formula, and in the struggle, the formula vanishes completely. Mr. Krabs goes into the office and sees the formula is gone. He blames Plankton, but Spongebob defends him when Plankton says it just disappeared.

Mr. Krabs decides to torture Plankton into telling him where the formula is by saying a knock-knock joke. Plankton doesn't understand until Spongebob starts laughing so much that Plankton can't stand it. Squidward Tentacles (Rodger Bumpass) comes in and says the angry customers outside want refunds. Without the secret formula, the whole supply of Krabby Patties is gone. Mr. Krabs tries to lead a mob against Plankton, but Spongebob blows a bubble that floats him and Plankton away, making Mr. Krabs think that Spongebob conspired with Plankton to steal the formula. Within seconds, Bikini Bottom transforms into an apocalyptic wasteland, with everybody wearing leather outfits and running around to create chaos. 

Burger Beard decides to end the story here by writing "The End" on the page. The seagulls are unsatisfied with this ending and demand that he continue reading. Burger Beard refuses, and one seagull struggles to get the book to find out the real ending. They rip a page out that falls into the ocean and lands on the home of Sandy Cheeks (Carolyn Lawrence).

Spongebob tries to convince Plankton to join him as part of a team to clear their names. They venture back into Bikini Bottom to find Patrick, caught up in the apocalyptic chaos by vandalizing his own home. Patrick sells them out and calls Mr. Krabs and the angry mob toward them. Spongebob and Plankton retreat to find Sandy, having gone mad from trying to figure out what the page with "The End" written on it means. She believes it is a message from the sandwich gods that are angry and have taken all the Krabby Patties. Spongebob and Plankton leave to go back to Spongebob's house to find Gary the snail having formed a snail cult in the house. Gary refuses to join Spongebob and sends his snail army after Spongebob. Spongebob flees despite the fact that the snails are too slow to chase after him.

Spongebob and Plankton hide out of town. While Spongebob sleeps, Plankton sneaks into his brain to try and get the formula, only to be repulsed by the cute and overly happy thoughts in Spongebob's head. After Spongebob wakes up, they get the idea to build a time machine to go back and prevent the formula from disappearing.

The two sneak into Plankton's restaurant The Chum Bucket to rescue Plankton's computer wife Karen (Jill Talley) as she is being held captive by the mob, with Patrick as a security guard. Plankton swipes a key from Patrick as he sleeps to go in and break Karen out. Using her, a photo booth, and other items, Spongebob and Plankton build the time machine. They go into the future where everything in Bikini Bottom is gone, with only a bearded Patrick waiting in the dirt for the Krabby Patties to return. Spongebob and Plankton time-jump again to a period where they meet an all-knowing dolphin named Bubbles (Matt Berry). Bubbles steps away to use the bathroom, leaving Spongebob and Plankton to watch Jupiter and Saturn collide. Bubbles comes back and shoots a laser at the two from his blowhole because he could lose his job. The two time-jump again to the moment before Plankton swiped the formula. Future Spongebob sticks his hand in the vault and grabs what he thinks is the formula, and he returns to the present time with Plankton.

Back above the surface, Burger Beard comes by a beach and pulls his boat onto land, where it turns out his ship doubles as a food truck where he serves burgers. He frightens the seagulls away when he pulls out a plate of hot wings.

Upon returning to The Krusty Krab, Spongebob shows Mr. Krabs and the mob the bottle with the formula. However, it's the bottle that Plankton tried to switch out, leaving a taunting note to Mr. Krabs. Sandy comes in and says they need to make a sacrifice to the sandwich gods. Spongebob decides it must be him that makes the sacrifice.

Everyone gets ready to sacrifice Spongebob when he says he smells Krabby Patties. Mr. Krabs then says he smells them too. He tells everyone to follow Spongebob as they travel far and wide to see that the smell is coming from above the surface. All the secondary characters leave, with only Spongebob, Patrick, Squidward, Sandy, and Mr. Krabs left (and Plankton hiding in Spongebob's sock). They try to figure out how they can make it above the surface, when Bubbles comes down and thanks Spongebob for helping him leave his job. He takes the gang in his mouth and shoots them out his blowhole to allow them to navigate above the surface.

The gang ends up on the beach and end up getting flung around the place until they hit Burger Beard's ship. They see that he has the secret formula, which he acquired after writing it down in the book. He is now selling Krabby Patties like crazy. He then writes down in the book to banish Spongebob and his friends to a small seagull island.

On the island, the gang finds the page that Sandy found, and Spongebob decides to write out his own plan to get the formula back. Plankton, having crawled out of Spongebob's sock, writes something down for himself.

The gang faces Burger Beard as superheroes. Squidward has a super-powered clarinet that he uses to drive the customers away from Burger Beard's ship. Mr. Krabs is now a robot that launches his claws to trap Burger Beard and keep him from writing anything else down in the book. Patrick uses his powers to manipulate ice cream and bring it to him. Burger Beard gets free and uses his ship to drive through town. Sandy, now a giant realistic squirrel, chases after him with the others riding on Mr. Krabs with his rocket boosters.

Burger Beard launches cannonballs at the gang. Spongebob, who has invincible bubbles, traps the cannonballs, until he gets distracted and is hit by one. Just when it seems that hope is lost, Plankton emerges with a massive body. He lifts up Burger Beard's ship and causes him to drop his book onto the grill, destroying it. He tries to get away, but Plankton helps Spongebob and blows into his bubble wand to stop Burger Beard. The pirate is forced to give up the formula, and Plankton kicks him far away onto the small island.

Spongebob writes the gang back home. With the formula safe and sound, Bikini Bottom returns to normal and Spongebob feeds everyone Krabby Patties. Plankton tries to make another grab for the formula disguised as Gary, but Spongebob sees through him and sends the real Gary after him. Plankton flees in fear from Gary.

Burger Beard, now stuck in the sand and surrounded by seagulls, decides to be nice to them, and they all sing the Spongebob theme song. Bubbles interrupts them and says he hates the song, and then challenges the seagulls to a rap battle. The seagulls beat him and they continue singing the theme song. Bubbles then decides that the song is pretty good.

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