At SpongeBob's house, him and Patrick are dancing. The music is shaking Squidward's house, so Squidward requests them to lower the volume. When they do not listen, Squidward plays a squeaky tune which sends SpongeBob and Patrick flying into Squidward's house and causes SpongeBob to hit Squidward, lodging his clarinet in his throat which makes Squidward make squeaky notes. When SpongeBob gets the clarinet out of Squidward's throat the reed is still stuck in him. They then go to Sandy who has a plan. She decides to go in a submarine, shrink herself (and the submarine), go into Squidward's body and retrieve the reed.
When Sandy goes to get some acorns and nuts from the Treedome she tells SpongeBob to guard the submarine. Patrick walks by and manipulates SpongeBob to guard the submarine from the inside. They go in there and guard it when Patrick presses the shrink button, shrinking the submarine. Sandy comes back and notices them. She then has to guide them to Squidward's brain. There, SpongeBob and Patrick start to hit parts of the brain, causing Squidward to lose self-control.
For a moment, SpongeBob and Patrick actually fight each other for control of the vehicle and land in Squidward's stomach, where the gastric acid starts to eat the submarine away. Patrick thinks of an idea: If Squidward can drink soda, then bubbles (gas) would surround them and it would refuel the submarine. Squidward drinks soda and the suddenly burps creating bubbles. They travel through the throat where SpongeBob removes the clarinet reed by doing what he was "born to do," dance. The reed is removed and the gang celebrates, but is cut short by the sound of the now angered Squidward. He demands them to leave his body and yells at them to "GO!" However, Patrick mistakes it for "grow" and hits the grow button while still being in Squidward's body.
Squidward is next seen at the Krusty Krab looking bloated and his stomach in the shape of a submarine. A flush sound is then heard, followed by Patrick, still stuck in the submarine in Squidward's body, claiming the toilet is clogged (again, apparently) Squidward groans.
The title and plot of this episode is a reference to the 1966 film "Fantastic Voyage," and it also parodies the 1987 film "Innerspace."
SpongeBob using the Whirlpool Spin to slice apart the reed is similar to the climatic battle in the 1986 anime show Ginga Nagareboshi Gin, where the titular dog decapitates the demon bear Akakabuto with the Zetsu Tenrou Battouga.
When SpongeBob says "Whirlpool spin!" his mouth does not move.
When SpongeBob cuts the reed in half, red electricity is seen for less than a second.
When Squidward burps, Sandy smells it even though she is wearing a helmet. However, she should not be able to because of the helmet.
In the first scene of the submarine, it looks like it is on an open platform, but later starting in the scene with SpongeBob guarding the submarine, it looks like it is in a room.