Here's my idea...
SpongeBob (with the help of Patrick and Squidward) chases Plankton across time and space to get the secret formula back, but Plankton also has another plan in mind to get rid of the three (mainly SpongeBob) so he could succeed.
Here are the world's...
W1; Bikini Bottom
W2; Jellyfish Fields
W3; Rock Bottom
W4; 450 million B.C.
W5; 1.999 million (Before Comedy)
W6-1; Middleville Times
W6-2; Bikini Gultch
W7; Bizarro Bottom
Nothing isn't normal in this universe/laws of physics don't apply there.
W8; Unemployed Sponge
This AU SpongeBob didn't get the job and ultimately became the Squidward of this AU.
W9; Injustice
Characters like SpongeBob, Patrick, and Sandy are inherently evil to an extent as they joined Mermaid Man's authoritarian government/dictatorial controlled ruled Bikini Bottom. In turn, characters like Plankton, Man Ray, and Dirty Bubble are inherently good to an extent as they would form a resistance/freedom fighter group to tackle and possibly overthrow Mermaid Man's government.
W10-1; Space Time Continuum
Ultimately, the trio ends up outside of time and space due to Plankton ejecting them outside of reality, but not to the point of going out of the Space Time Continuum.
W10-2; Doodle Dimension
The trio manages to get back into time and space, ultimately popping up here where an old foe awaits.
W11; Apocalypse: March 17th 4017
The trio is finally able to get back to what they think is their reality, until they realize that this is a dystopia (an even worser one than Injustice) where Bikini Bottom is unrecognizable and the population has no hope for freedom or livelihood (the plot twist would be revealed here).
W12; Bikini Bottom: 3 days later
The endgame takes place here...
Bonus (W13); March 17th 4017: Utopia