The Ugly Barnacle/WMG

The Ugly Barnacle actually happened within the universe of Spongebob SquarePants
There was an ugly barnacle, and it did kill an underwater civilization of men and merpeople. The only survivors were either gods (Neptune) or superheroes (Mermaid Man and Barnacle Boy). Yes, yes, this inspired Atlantis. The underwater dead became so infected and mutated by the fallout of ugly that they spontaneously resurrected and became sentient. Yes, yes, Bikini Bottom is just like a past-Zombie Apocalypse civilization. And that is why Spongebob sometimes looks like an Eldritch Abomination.
 * Jossed, because everyone died.
 * Not necessarily. "Everyone" could refer to everyone in a specific REGION, and it may not affect Bikini Bottom.
 * Furthermore, even if everyone dies, who says they have to stay dead?
 * Just got an idea from that - the residents who died from the barnacle's ugliness died, and then they, through some process, came back to life as a form of zombie. Over time, they became the citizens of Rock Bottom.

In addition, Barnacle Boy got his name because the ugly barnacle killed his parents.
Mermaid Man took him in as an adopted son, where he tried to prevent such a tragedy from happening again.
 * For this to be true, it would have to mean that Barnacle Boy was elsewhere when the Ugly Barnacle struck. I support this theory.
 * Or Barnacle Boy could in fact be related to the Ugly Barnacle, which might explain his human-like appearance. Perhaps the residual effects of "the ugly" also gave him his superpowers.

The Ugly Barnacle is a metaphor for the atomic bomb.
It worked for Braid.

The story is a victim of mistranslation.
The ugly barnacle was actually so ugly that everyone dyed...it pink, in order to make it cuter.

The barnacle was actually not ugly at all.
Patrick is dumb.

The barnacle is Cthulhu.
This explains many things, like its presence underwater, its ability to kill everyone, and why it's so ugly. Describing it as a barnacle is simply the closest comparison one can conceive to describing its true form.

The barnacle is some kind of sea Gorgon.
Well, being turned to stone kills people.

The Ugly Barnacle is an abridged version of the events of Neon Genesis Evangelion.
The story revolves around a character who is "ugly", which can be interpreted as someone who feels that they aren't worth anything. The "The End" is a reaffirmation that "The End Of Evangelion" has occurred.
 * To wit.
 * After The End Of Evangelion happened, the world was rebuilt. Kaworu rose up from the LCL sea and emigrated to the Bikini Bottom, pretending to be a dumb starfish. He became a friend of Spongebob and told The Ugly Barnacle tale to cheer him up. It did not work.

The Ugly Barnacle is the anime Neon Genesis Evangelion itself.
Disturbing imagery (best expressed as "ugly" without traumatizing one more individual), pessimism, and The End of the World As We Know It were way too much for everyone to bear. As the anime hit episode 23, some were so disgusted with the plight Rei had suffered, that they instantly died from heart attack. A few even went insane and began to perform surgical abortions on themselves. By the time of End of Evangelion, People committed mass suicide, accidentally killed themselves while popping their eyes out, starved to death because they couldn't stand eating something, or simply died from heart attack en masse. Fortunately, "everyone" in this tale meant every single person living on the landmass, so the marine life was safe. At least for now.

The Ugly Barnacle is Man.

 * Man kills things with ugliness?
 * Don't you mean MMMAAAANNNN?

The Ugly Barnacle was the demons.
And then, everyone turned into zombies.
 * The End! ^D

The Ugly Barnacle brought about the previous Apocalypse.
And we are all descended from it because it repopulated the world.
 * All the organisms on earth used to be incredibly beautiful... until the Ugly Barnacle killed them.

The Ugly Barnacle is the Walpurgis Night.

 * Alternatively, the Ugly Barnacle is Kriemhild Gretchen, which is uglier than Walpurgis Night and intends to absorb everyone's souls.

The Barnacle isn't actually a barnacle, but instead the Dark Dragon.
Its nightmarish, twisted visage caused

Patrick wasn't telling a narrative tale, but rather recounting a history
All of it really happened. Indeed,it happened on dry land, and the "barnacle" was a human and the story took place in the (to us) present day, but the story was slightly warped over time to make it a barnacle. The few survivors (remember, it was warped in the telling, so not everyone died) retreated to the seas and over the millennia became more biologically compatible with marine life (perhaps some sort of machine was created to accelerate and manipulate genetic change). They remember almost nothing about their land origins save a few myths, including the story of their past society's downfall, and have only recently reached a point where their society parallels what modern humans have. Sandy- and probably all squirrels, really- is so strong because any creature would have to be to survive on land, as most of the world is a nuclear wasteland. Patrick is a keeper of ancient lore for...some reason. Maybe he's smarter than we think, or perhaps nobody else wanted the job. Patrick is warning Spongebob of the dangers of the past so he will make efforts to increase his good looks and so avert a repetition of the past.
 * You, Troper, are a brilliant scholar. I salute you and your works to further the knowledge of mankind.

The Ugly Barnacle is Haruhi Suzumiya.
Explains a lot, doesn't it?

The Ugly Barnacle killed everybody.
He was shunned for his ugliness, causing psychological damage. He wanted revenge, and sought the power to take it upon all who rejected him.
 * So, the Ugly Barnacle is Carrie? Hell, I want in!

The word "barnacles" is a curse word in the Spongebob universe because of the Ugly Barnacle killing everyone, so the word is used when something is ugly, foul, or a generally bad situation.
Hey, the word's context had to come from somewhere.
 * Fridge Brilliance, anyone?

The Ugly Barnacle is a time lord
It explains how everyone died, and yet Patrick was still around to tell the story. Alternately, Patrick is a time lord, and the events of the Ugly Barnacle haven't happened yet.

Additionally, every human being is descended from Rory.
Rory has died six times already. He's not going to let a 7th death stop him.

Patrick was exaggerating.
How could EVERYONE die, if we are alive right now?

There is an off screen character NAMED "Everyone"
And the Ugly Barnacle kills "Everyone" - the character with that name.
 * So it's more of a Who's On First? situation, then?

The story takes place in Purgatory...
...and "Everyone" was an alias being used by Jesus, who died.

The story did help Spongebob
But he was in denial of it because it wasn't the story he was expecting.

The barnacle was phone
It went insane from being an outcast from society due to its ugliness. It was so crazy that it went on a killing spree, and one of the victims was the girl's father. And because it was so crazy, the barnacle then believed that IT was the girl's father, which is why it said to stay away from her, and referred to her as its daughter.

The Barnacle was Aizen
Being ugly was part of his plan to kill EVERYONE
 * Aizen, ugly?

The Barnacle Was Once a Man.
Or maybe he was a barnacle man. Or maybe he was just a barnacle. But he was still ugly. So everyone burninated themselves.

Patrick was/is the barnacle
Patrick is an eldritch abomination who is recalling personal experience. He once lived on another planet, in another dimension, etcetera...His true form (i.e. his 'ugliness') killed everyone on said planet, in said dimension, etcetera...including his friends, loved ones, everyone! So riddled with guilt, and so wrought with grief, he came to Bikini Bottom, hoping to start a new life, disguising his true form. When Spongebob was upset over his own 'ugliness' Patrick reinvented his own tragic tale into a harmless children's story...it didn't help at all...That may be because he slowly went mad from the guilt/grief, or possibly hiding his true form. Subsequently, the story wouldn't exactly...convey...the desired effects. Either way, he is subtly telling Spongebob to get over himself, as HE knew firsthand that Spongebob was being dramatic. He has every right to be indignant. This also may coincide with his being a time-lord. This troper likes to believe his real name is Szaellcaraeth.
 * This also explains why later in the episode, Patrick was so worked up over thinking he had become ugly again.
 * This premise has now been made into a story- The Ugly Barnacle: The Tale of Szaellcaraeth

The Barnacle was only ugly from one point of view
Many barnacles travel on the bodies of larger animals, either in parasitic or communal relationships. This means that it might have been introduced to a radically different area. The standards for ugliness were different, or locals simply couldn't handle the sheer difference. This would be similar to how a simple butterfly was ugly enough to nearly make Bikini Bottom Go Mad From the Revelation Cthulhu-style in another episode, despite not causing direct harm. Ironically, the barnacle might not have even been aware of what was happening, as barnacles have limited, usually short range, senses.

Not everyone died directly from The Barnacle's ugliness
Maybe he looked at himself in the mirror, went crazy because despite all his efforts to look good, and decided to kill everyone so that he would be the most beautiful person in the world. Alternatively, just a few people actually saw the barnacle and did go crazy, killing everyone else. One of these people might have written the whole story down, which is how it survives to the present day.

Everyone DID die, and they're all living in the Afterlife.
After all, even if the Barnacle DID reproduce, his offspring would also have died from the sheer ugliness.
 * This could also be fridge horror. After all, if he was so horrific everyone died then at least they would have been killed moments after gazing upon his ghastly visage. However, since they can't die any more they are now forced to look at him for all eternity.

The Ugly Barnacle is Sonic the Hedgehog 4
No other charcters than Sonic and Eggman are in the game, and it was poorly recieved.

The Ugly Barnacle is Zim

 * Zim gave up taking over the world, so he just killed everyone in the sea, and took it over.
 * He's ugly, cause he's an alien, an Irken to be exact

We ALL have two lives each
Just that thanks to the main character, our first lives are used up.

The Ugly Barnacle is the Time Crack.
Because what else could make it so everyone died? After all, the cracks
 * But if the cracks destroy timelines, they never lived to begin with, so how does the narrator know that they died?

The story was supposed to convey An Aesop about inner beauty
The ugly barnacle was a Complete Monster whose inner "ugliness" led to everyone dying at his hands. Patrick just didn't tell it right, because, well, he's Patrick.

The Ugly Barnacle is why Plankton has a phobia of whales
Barnacles are commonly associated with being stuck on whales.

The Ugly Barnacle is the reason "barnacles" is used as a form of profanity
The story, and thus the origin of the term, was lost until Patrick rediscovered it.

The Ugly Barnacle is global warming.
The global warming will raise the sea level, drowning many cities. Meanwhile, it will make natural disasters happen more frequently and will make agriculture harder, reducing food production. In the end, the climate change is so severe that we all starve to death or get killed in wars for resources.

Patrick wanted to say that Spongebob was not as ugly as the Barnacle.
At least, Spongebob does not kill everyone with his ugliness. Sadly, Patrick was not a good storyteller.

The Barnacle is a Daemon Prince of Malal.
with nothing to gain and not a trace of rage, it butchered a world simply because it was there. certainly fits the bill.

The Ugly Barnacle is a tale about The Precursors from the Starcraft universe.
The Ugly Barnacle is thought to be either Sarah Kerrigan, Arcturus Mengsk, Zerg/Protoss Hybrids, the Void or some combination of the four.When the storytellers were asked how they looked like, they couldn't describe those individuals as anything but ugly-looking barnacles. Hence the oversimplified tale of how the Precursors fell.
 * Kerrigan: An extremely powerful psychic and possibly a Humanoid Abomination, she destroys the universe with her immense powers, driven to insanity by her troubled past life and identity crisis. (as a conscripted Child Soldier, an infectee, et cetera.)
 * Mengsk: A cruel and power-hungry dictator, Mengsk somehow develops a technology to create a Hive Mind of advanced robots that can replace human labor forces, so he exterminates his subjects with virus, killer bots, and other nasty stuffs. He's either the Hive Queen of the newly built robot empire, or he is killed in the process of replacing humans with robots.
 * Zerg/Protoss Hybrids: They eat every atom of organic matter in the universe.
 * The Void: It divided the universe by zero.

The Ugly Barnacle is the Second Law of Thermodynamics.
So powerful, so irresistible, so devastating.

[[WMG: The original barnacle was actually female, this fact was lost due to mistranslation.