WMG / The Bikini Bottom Horror

SpongeBob's destructive actions will eventually be undone and reverted by a character we haven't met yet.

But who? There are a few possibilities.

• The epilogue reveals that Neptune has somehow gone missing. If there's a sequel, perhaps the plot might involve the protagonists seeking him out and asking him to use his powers to undo the Bad Future that SpongeBob caused. Because if anyone can fix this, it's an actual god like Neptune.
• The Flying Dutchman. He's a borderline Reality Warper who deals in terror, and he probably won't be too happy if he finds out someone else is has destroyed Bikini Bottom and is now ruling it with an iron fist.
• Man-Ray or Dirty Bubble. With Mermaidman and Barnacleboy both dead, "Mermaid-Squirrel" (aka Sandy) in exile back in Texas, and SponeBob already ruling Bikini Bottom, what are a couple of supervillains to do? This could lead to an interesting Enemy Mine scenario with Sandy as the two former enemies find a common goal.
• David Hasselhoff could save the day again. Enough said.

SpongeBob didn't plan the Tortured One's rampage at all.

It's pretty commonly accepted— though not confirmed by Word of God— that SpongeBob deliberately planned the Tortured One to destroy the Krusty Krab and the Chum Bucket, allowing him to be revered as a hero and take over with his own restaurant. While there's certainly a lot of contextual evidence in the story suggesting this, there's also a possibility that this isn't what happened.

First off, consider what Sandy is going through when she questions him about his role in the disaster. She clearly shows a lot of symptoms of PTSD during the epilogue: she clearly suffers from a major case of Survivor Guilt, is traumatized by the fact that her friends are all either dead or warped beyond recognition, and even seems to go into a full-fledged flashback when she returns to Texas. People with PTSD often lose trust of their friends and see malicious motives behind other people's everyday actions that aren't really there. So it's possible— obviously not confirmed, but possible— that the whole disaster really was an accident, and what we see in the epilogue is simply Sandy's traumatized mind making it even worse.

But if that's the case, why would SpongeBob be going to such lengths to cover it up? Him having masterminded the whole thing is definitely one explanation. But another possible explanation is guilt. When Sandy leaves the Pretty Patty restaurant after accusing him of causing the disaster on purpose, SpongeBob looks sad; is this because he's disappointed she isn't seeing things the way he does, or could it be because he realizes how far he's fallen and can't bring himself to let everyone know the truth? It's possible SpongeBob may be just as traumatized by the disaster as Sandy is.

Consider how he acts in the epilogue compared to the main story. He puts on a cheerful facade, but his mood rapidly shifts from scene to scene, he’s prone to little outbursts of anger (towards Sandy when she asks about the undercooked patty), and he refuses to mention or acknowledge the massacre he caused. Those are all classic signs of trauma. He hates what he's become, and he's willing to go to any length to make sure no one finds out about the terrible thing he did, which is why he suddenly pushes back so harshly when Sandy brings the subject up.

If there's a sequel, there will be a "Guilty SpongeBob", much like there was a "Guilty Patrick"

In the epilogue we see that SpongeBob has staffed his Pretty Patty restaurant with clones of himself. Assuming the above WMG isn't true, and SpongeBob really did plan the Tortured One's rampage, it's possible that at least one of those clones might begin to have second thoughts about what the original SpongeBob did. He might even betray the original SpongeBob and the other clones and help Sandy and/or Squidward expose the conspiracy that destroyed Bikini Bottom.

• Sequel has been confirmed.