The Krusty Krab opens at a seemingly average morning and SpongeBob is extremely happy. He gets the Krabby Patties ready and soon gets an order of two Krabby Patties plus an insult from Squidward, which is to no effect. His excitement eventually causes him to accidentally throw his spatula into the ceiling and when trying to get it out, he falls, nearly being injured by scissors and swords.
Upon landing, all is well but he trips on tartar sauce. His thumb drags across the wooden floor and rams into a small slab that breaks in half, giving him a splinter that immediately makes his thumb red and swollen. His weak arms keep him from getting it out and even biting it doesn't work. The customer that ordered earlier is turning impatient and the splinter keeps SpongeBob from holding the spatula needed to serve him. He decides to tie it on his nose and Squidward soon finds out about it.
Squidward then convinces SpongeBob that he will get sent home by Mr. Krabs if he sees the splinter and flushes his hat and spatula down the toilet. SpongeBob begs Squidward not to get him sent home, but is unsuccessful. Squidward also hints that he'll tell Mr. Krabs about the splinter. After Squidward gets his full enjoyment about the situation, Mr. Krabs drives a customer away with his cheap behavior.
SpongeBob calls Patrick to get treated for it, but the treatment only ends up with his splinter further into his thumb, making it swell more and even infecting it. SpongeBob soon runs into Mr. Krabs and Squidward. Mr. Krabs soon sees the splinter and takes it out, curing him and causing an eruption of pus to impact Mr. Krabs.
Squidward discovers that he could get sent home early and still get paid by getting injured, called worker's compensation, so he tries to injure himself, only to find out that his shift had ended two minutes ago.
It's unkown why the Krusty Krab has a box of swords.
When Patrick puts SpongeBob's foot in his mouth, you can see his shoe and sock is removed. When the scene cuts back to SpongeBob and Patrick, the sock is still on his foot, and when Patrick removes the foot from his mouth, the shoe is also on.
This is the second time SpongeBob has something stuck in the kitchen, the first time was in "Employee of the Month." Ironically, both started at the grill and became stuck on the ceiling.
This is the second time Patrick impersonates a doctor. This first was "Suds." At both times, he is confident on how to do his job. Though, Patrick should be arrested for impersonating a doctor (for being a quack doctor), as Sandy says in "Suds."
In "Suction Cup Symphony," SpongeBob would be the doctor instead and Patrick doesn't know this during "The Splinter."
If one would look closely when the spatula is in the freezer getting the Krabby Patties, there is a frozen caveman.
When Squidward finds out that SpongeBob got injured on the job, he flushes SpongeBob's hat and spatula down the toliet. After getting an "appointment" with Patrick, SpongeBob hears Mr. Krabs coming. When Squidward and Mr. Krabs enter in the kitchen, SpongeBob hid his right hand in his hat, so SpongeBob must have had a spare hat.
This is one of the few episodes where SpongeBob's skeleton is shown despite being an invertebrate ("Squid on Strike" is another example, where this happens twice in that episode).
In real life, it's impossible for splinters to grow as big as SpongeBob's in this episode. They can't heal as fast if they were infected either.
When Squidward is squishing his "hand" together, pretending to crush the customers head, this is a reference to something people sometimes do when they are bored. It was started by the comedy scout "Kids in the Hall," on an episode of a show with the same name.
When Patrick put the garbage compress on SpongeBob's thumb, it turned dark purple and green pus came out of it. However, when SpongeBob later showed Mr. Krabs and Squidward his thumb, it was red in color.
When SpongeBob opens the box he took out from his pants, it was halfly in the table, but there clearly wasn't a hole there before he put the box down.
The kitchen ceiling suddenly became much higher when SpongeBob realizes his spatula was stuck in the ceiling.