A bubble is a soap or air structure, usually round, that either comes from a bottle filled with bubble soap, movement of a character underwater, or as a transition sequence between scenes. They first appear in the episode "Bubblestand."
In "Squid Defense," karate chop transitions are used instead of the regular transition.
In "SpongeBob's Place," after Mr. Krabs builds a trench filled with molten lava near the Krusty Krab door, the customers step over him to go to SpongeBob's Place. After Krabs' plan to keep his customers backfires, the transitioning bubbles to the next scene are replaced with the lava bubbles.
In "Suds," SpongeBob gets the eponymous disease, a sickness that causes him to blow pink bubbles out of his holes.
In "Wormy," SpongeBob blows a bubble to encase the newly-transformed Wormy - who had just become a monarch butterfly - therefore, allowing him to survive underwater.
Atlantis' prized possession, the oldest-living bubble, has been desired by SpongeBob and Patrick to take the picture of the bubble. They took the picture of the bubble, and though they popped it, it was not the real bubble. The real bubble was under LRH's possession. After Patrick took a picture of it, the bubble popped and LRH summoned his guards to seize them. Plankton became the replacement of the bubble.
SpongeBob and Patrick make bubbles from a bottle of spicy sauce in "Bubble Troubles."
In "It Came from Goo Lagoon," several goo bubbles come up from Goo Lagoon. SpongeBob, Patrick, and every other Bikini Bottomite misinterpret the substance to their uses. Sandy warns that the goo bubbles could be dangerous, where they initially disregard her. Upon hearing this, Plankton plans on using a large one for his needs and uses his submarine to find it. After, Plankton vows that he will pop the bubble down to Bikini Bottom if he does not have the Krabby Patty secret formula. Despite various attempts from the gang to end his scheme, Plankton manages to keep the bubble long enough. Mr. Krabs then gives Plankton a fake formula, where the tiny cyclops pops the bubble to them. After Plankton's defeat, Mr. Krabs profitably cleans everyone up with the Bubble Man created by SpongeBob.
In "Burst Your Bubble," SpongeBob blows bubble boats for many Bikini Bottomites, due to the fact that he could not get a license for a real boat. Mrs. Puff later realizes that regular boats are forbidden and that it is now required to drive in a bubble boat. Mrs. Puff then attempts to gain her bubble boat's license, with no success. Later in the episode, most of the bubble boats end up popping causing the various bubble boat drivers to resort back to driving a solid boat.
The episode "Bubbletown" features an entire town made of bubbles called Bubbletown, where everything and everyone is made of bubbles. Bubble Buddy, his wife, and his son Shiny live here.