Squidward is dreaming he is a great musician. Suddenly, his alarm clock goes off, waking him. He prepares for another day at the Krusty Krab. While SpongeBob gets ready to go to work, he sees Squidward and asks him why he is playing his clarinet. Squidward says he is practicing for his performance tomorrow. Squidward keeps walking to work while SpongeBob visits Sandy. He finds Sandy with a machine that can transport things. Sandy shows SpongeBob how it works by teleporting an apple to Mrs. Puff's desk. SpongeBob asks Sandy if it can transport him to the Krusty Krab. She allows him to try it. When he gets there, part of Squidward's arm gets stuck in him.
Suddenly, the machine malfunctions, and SpongeBob and Squidward are transported back morphing them together. Sandy sees what has happened and is terrified. When they walk out, SpongeBob has his normal head/body, while Squidward's head is sticking out of the upper left. SpongeBob's left arm and right leg are Squidward's. They are in control of each other's arms, as well. Squidward tries to get out, but he cannot. He is scared of the fact he and SpongeBob are stuck together. SpongeBob says they can be together forever now, scaring him more. Squidward asks Sandy to do something. She decides to zap them back in the transporter. She zaps them to a school, a hospital, and Mars, but they are still stuck together. Squidward says she has to get them unstuck. Sandy tells Squidward she was working on a new invention, but it is not ready. He tells her to hurry because he cannot stay stuck to SpongeBob.
She tells him to stay calm, and she will continue working on it. Squidward and SpongeBob are riding to work on a bike. SpongeBob says he will drive, but Squidward keeps getting hit by the wheel. They crash into the kitchen and Mr. Krabs asks what happened. They stand up revealing their morphed body. Mr. Krabs just tells them to get to work. They try working, but they cannot because they are stuck together. Mr. Krabs kicks them out and tells them to not come back, until they fix their problem. SpongeBob says they still have each other, and Squidward angrily says that is how they ended up like this in the first place. Squidward practices playing clarinet while SpongeBob is sad. A surfer guy passes and says "Rock on, Freaky Bro." They run over to Sandy's and ask her if she is found a way to fix them. Sandy says she has invented the Molecular Separator Ray. Squidward is ready to be free, but Sandy says she is not finished. She says she will probably have it ready the day after tomorrow. Squidward frantically tells her he has a performance tomorrow. So she tells him she will have it ready before he goes on. SpongeBob and Squidward try to go to their own houses, but they cannot due to being stuck.
Squidward tries by force, but it pushes their houses together. At the clarinet performance the next day, Squidward is wondering where Sandy is. He thinks about giving up, but SpongeBob tells him this is his big chance to be a star. He decides to wear a cloak in order to hide SpongeBob. He starts playing his clarinet, upsetting everyone. A loose nail pulls the cloak off, revealing their secret. Amazingly, the crowd loves and starts cheering. Squidward finally knows what stardom fells like. Suddenly, Sandy shows up and tells Squidward she finished the device. Squidward tries to tell her not to, but she separates the two, displeasing the crowd. Squidward starts playing his clarinet again, but everyone hates the sound of it.
They leave in anger and disgust. Squidward says his one moment of fame is gone. He yanks the machine from Sandy and tries to reverse it. Sandy tries telling him that it is a very sensitive device. Suddenly, the machine breaks and Squidward is morphed. Squidward is seen at a psychiatrist's office. The doctor asks Squidward what the problem is. Squidward says it all started when he was born. It is revealed that Squidward was morphed together with SpongeBob, Patrick, Sandy, Pearl, Mr. Krabs, and Mrs. Puff. He now looks even worse than before.
In some areas of Kentucky, the ending scene where several different characters are fused with Squidward was at one point cut out, as cable provider Insight Communications has been known to censor explicit content from television.
Squidward's hair in his fantasy is similar to Kenny G's.
When SpongeBob SquarePants and Squidward were fused together is a parody of the 1986 science fiction horror film The Fly. Also, the teleporter Sandy made is similar to the one in the movie.
A similar fusing occurred in a Star Trek: Voyager episode, when Tuvok and Neelix fused due to a teleporter incident into the character Tuvix. As the case with SpongeBob and Squidward, Tuvok and Neelix are quite dissimilar and could hardly be called friends. Also coincidentally, Paramount produced this episode 9 years before the SpongeBob episode was made.
SquidBob TentaclePants' premise that two characters with opposite personalities are conjoined together is also similar to the idea of CatDog TV show. Steven Banks, who co-wrote this episode, was also a writer for CatDog.
When SpongeBob and Squidward—still fused together—walk through the Krusty Krab, Lenny, in bewildered confusion, drops his Krabby Patty, picks up a bottle of hot sauce, and says "I've gotta lay off the hot sauce," which is a play on words with the phrase "lay off the sauce" (regarding "sauce" as alcohol).
The ending, where Squidward is fused with everyone, could be a reference to Tetsuo's demise in the 1989 film Akira.
Patrick appears at the end of the episode but does not speak; though, he was heard cheering after the audience sees SpongeBob and Squidward fused together. Even though Patrick was heard cheering in audience, he is not listed in the credits.
At the point where Squidward is speaking to Sandy and says "I can't stay stuck to that yellow freak" and it zooms in on SpongeBob, the tentacle arm is colored yellow, instead of the usual bluish color.
At the recital, when SpongeBob convinces Squidward to perform fused, he uses the sponge arm instead of the squid arm.
This may be due to the fact that Squidward was morphed into SpongeBob's body, so SpongeBob had control over them both.
When SpongeBob and Squidward go to their houses, they use their own arms instead of each other's arms.
In the part where Nat holds his barf, Sandals' eyes are not attached to his body.
Although Larry was in the hall when Squidward messed up the Molecular Separator Ray, he is nowhere to be seen in the ball of fused characters.