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Sandy, who has let her competitiveness and recklessness get the best of her, decides to feed the jellyfish in Jellyfish Fields Frankenstein Fish Food, which causes them to mutate and become bigger and more dangerous. Sandy uses a super suit to catch all of the jellyfish, however, because of sandy and her super suit, Jellyfish Fields gets destroyed. This causes Sandy to finally realize that she went too far and leaves Jellyfish Fields. After returning to her treedome, Sandy starts meditating to calm herself down, however, unbeknownst to her, the jellyfish end up combining with each other to become a bigger and more monstrous jellyfish.
The Giant Jellyfish is later seen chasing SpongeBob and Patrick towards Sandy's treedome. The duo ask Sandy to stop the Giant Jellyfish, however, she refuses because she has decided to take on a nonviolent demeanor after what she had done earlier. The Giant Jellyfish lifts up the treedome and floods it with water, and it then crawls inside and begins to torture the trio. Sandy tries to use music to calm down the Giant Jellyfish, but it becomes more enraged, and proceeds to squash SpongeBob and Patrick. After this, Sandy decides to abandon her new pacifistic nature and goes back to being the aggressive squirrel she was previously in order to save her friends from the Giant Jellyfish.
Sandy tries several different methods to defeat the Giant Jellyfish, and she eventually success in doing so by charging inside of it and beating it from the inside, which causes it to explode into a bunch of normal and less dangerous jellyfish. At the end of the episode, the trio are shown to be back in Jellyfish Fields, with Sandy acting less competitive and aggressive this time, until a jellyfish stings her and makes her mad.
The Giant Jellyfish later makes a cameo in the Kamp Koral: SpongeBob's Under Years episode "The Jelly Life". When SpongeBob tells Sandy that he only knows about jellyfishing from what he has read in comic books, he holds up three comics. One of them is titled Attack of the Killer Jellies and the cover has a picture of the Giant Jellyfish riding a wave.