SpongeBob and Patrick are jellyfishing at Jellyfish Fields. Then, while running, SpongeBob notices that Patrick running toward a sign that says "DANGER CLIFF" and tries to warn Patrick. Patrick literally runs through the wooden sign and off the cliff (while still trying to read the sign). SpongeBob finds the top of Patrick's head and screws it back on.
Suddenly, Patrick's brain starts working in ways it never had before. Patrick seems to be interested in nature, work and almost any music when he is intelligent. He loses interest in all the things he and SpongeBob enjoyed, and actually has fun with Squidward and Sandy, until driving them both away with his patronizing attitude (he tells Squidward to find himself a new musical mentor because his horrible music annoys him and tells Sandy that she does not have the ability to solve "remedial" equations, causing Sandy to shout "I liked you better when you were a barnacle head!").
Since he is too hard even for them, Patrick wants to have fun with SpongeBob again. He tries many solutions to solve his problem, such as comparing himself with SpongeBob, meditating, doing research on Squidward, reading books about smarts, and even growing hair, but none of these things work.
Eventually, he kidnaps SpongeBob and tries doing all the activities he used to do. When this doesn't work, he tries to redo his actions by running through the wooden sign (which was just repaired) and falling off the cliff again. Patrick, still smart, finds out that the forehead SpongeBob had found could not possibly have been the original. They both find out that SpongeBob had found Brain Coral rather than Patrick's forehead. They find Patrick's original forehead and SpongeBob puts it on Patrick, which makes him normal again. Then, Patrick starts to burp, and SpongeBob and Patrick make loud, obnoxious noises and start giggling and running off.
Spongebob and Patrick are seen sandboarding, making this the third appearance of sand mountain since "I Had an Accident."
In the episode "Squid's Visit," Patrick said that Squidward only went to his house to take back some stuff that he borrowed, but in this episode, Squidward was at Patrick's house testing his brain fluids. It is most likely that this episode took place after "Squid's Visit."
The episode is similar in plot to the novel Flowers for Algernon in which the protagonist gains intelligence quickly, but then wishes it gone because of the way others see him.
Squidward plays a song that Patrick identifies to be titled Cornelius Pufferfish's Opus 67 "Symphony in Blue" - a possible reference to a song of the same name on Kate Bush's album Lionheart. It could also be a reference to George Gershwin's Rhapsody in Blue.
The first thing Patrick says after having his brain connected is, "I find all this laughter highly illogical," a tribute to Spock's famous phrase on the original Star Trek series (which Paramount also produced).