It is a typical day at Goo Lagoon and SpongeBob and Patrick are having fun. Suddenly, large purple volcanic Mucus Bubbles, also known as "Super Bubbles" arise out of the lagoon. They came out of a crack at the bottom of the lagoon. Two bubbles approach SpongeBob and Patrick while they are about to drown at sea. They bounce the goo bubbles like a ball on seawater, accidentally hitting fish swimming with a floater, a surfer, and a cheerleading-style posed fishes. Meanwhile, Sheldon (Plankton) tries to sell his chum from a wheelbarrow when Squidward smashes him with an umbrella. SpongeBob and Patrick use their Mucus Bubbles to likewise bounce and smash Squidward and his belongings.Plankton thinks that it is Karma and he notices that SpongeBob and Patrick are bouncing the goo bubble like a ball. He doesn't know what it is and tries to ask Squidward but Squidward leaves him and angrily scolds SpongeBob and Patrick.Just as SpongeBob and Patrick were going to use the goo bubbles to bounce like a ball, Sandy approaches them. Sandy tries to explain to SpongeBob, Patrick, Squidward, the Bikini Bottomites, and Plankton, that the bubbles are dangerous. She says that they are safe when stable, but if unstable, it can coat all of Bikini Bottom in a poisonous goo. Plankton hears this and builds a machine to find a bubble large enough to destroy the entire city, as most are rather small. Then he goes under the water in a ship to find the crack where the bubbles are coming from.
Meanwhile, more bubbles begin to arise from the lagoon, and the Bikini Bottomites begin to use the bubbles, although Sandy said it was dangerous. SpongeBob and Patrick continue to use the goo as bouncy balls. Squidward begins to use the goo as a hairdo. The other citizens continue to use it for their own purposes as well. Perch Perkins begins to report for the Bikini Bottom News with Johnny. He states how the gooey Mucus Bubbles are popular at Goo Lagoon. While on the air, Sandy, now going partly insane with her theory, says how the bubbles were dangerous again. Everybody still thinks she is wrong, but soon she will be right. Plankton continues on his quest to find the ultimate Mucus Bubble in his ship. He is set to find the crack at any cost. Soon, he finds it. Plankton, as well as Karen, widen the crack and unleash the largest Mucus Bubble. It rises out of Goo Lagoon, and everybody now agrees with Sandy.
The trio examines the bubble and realize it is dangerous. They need to stop it with supplies from Sandy's Treedome SpongeBob, Patrick, and Sandy proceed to her treedome. However, Patrick gets swept into the bubble, controlled by Plankton. The duo gets into Sandy's submarine at her treedome, then proceeds to save Patrick. They soon find the giant bubble and they tell Patrick to get in the Submarine but Patrick refuses, so they send down a crane to grab Patrick, who is sitting on the goo. Patrick is grabbed into the submarine, and then the three prepare themselves to stop the bubble. They soon discover that Plankton is controlling the bubble, after they see his ship. The recently reformed trio pursuit Plankton around the bubble. They oddly catch him seemingly easily. Sadly, Plankton outsmarts the trio and sends them off the bubble. He also destroys Sandy's submarine. The trio then pursue the bubble on foot through downtown Bikini Bottom. They end up at the Krusty Krab. SpongeBob, Patrick, Sandy, many Bikini Bottomites, and Mr. Krabs confront Plankton and the bubble in front of the Krusty Krab and Chum Bucket. Then, they attempt to send the bubble away, and foil Plankton's plan. Their attempts are failures, however. Plankton then demands the Krabby Patty formula or else he will pop the bubble, and coat the entire city in a poisonous goo. Left with a choice of giving up the formula or being chased by an angry mob, Mr. Krabs reluctantly surrenders and gives him the "formula." Plankton outsmarts them again, and pops the bubble anyway. The city is now covered in a poisonous goo. Plankton proceeds to read the "formula " on his ship. It reads, "The Only Ingredient Is... T.N.T."! He realizes the formula is fake while the T.N.T explodes, ruining his plan. Mr. Krabs, covered in goo, thinks everything is back to normal. Sandy corrects him, with the fact that everyone and everything in Bikini Bottom is covered in goo, and says that it is a "disaster." Mr. Krabs makes a plan to clean everybody. He uses soap bubbles to clean everybody and everything in town, while still making a profit.
In May 24, 2014, It Came from Goo Lagoon had a playable version with The Goo From Goo Lagoon online game.
The goo bubbles in this episode are purple, despite the title card background making it seem like they would be green.
SpongeBob and Patrick run back and forth from the water wave similar to how they ran back and forth from their houses in "That Sinking Feeling."
Patrick, once again, had a nose in this episode.
Plankton sells chum from a cart in this episode which is similar to how he sold chum from a box in "Drive Thru."
The Tanning Mirror seen in this episode is different to the one seen in "Mermaid Man and Barnacle Boy." Also, in both episodes, Squidward is the one who uses it.
When Patrick Star hands are covered with goo, Patrick pulled his arm off and it didn't grow back. Normally the limbs of a starfish do grow back. Patrick's limbs in the episode "Karate Star" did grow back, however.
It took a long time to grow back in that episode, so it is probably that it would have taken too much time to wait in this episode.
Patrick's "toupee" bears a resemblance to Elvis Presley's hair.
When SpongeBob and Patrick are bouncing on the goo bubbles right before they hit Nat, SpongeBob is shown and then Patrick shown ahead of him, but when SpongeBob bounces over Nat and when Patrick hit Nat, Patrick is behind SpongeBob.
Both Patrick and SpongeBob's clothes change from their swim outfits to their normal outfits without it being shown.
The button on Sandy's suit that opened up the projector was placed between the top of the zipper and the zipper itself.
When Bill jumped in the trash can, he was dirty and then turned from green to blue.
When the Super Goo bubble is shown between the Krusty Krab and the Chum Bucket, the path leading from the Chum Bucket to the road is missing.