The film begins with a live action credit sequence, in which a group of pirates retrieve tickets to The SpongeBob SquarePants Movie. The pirates then go into the movies and then the film then cuts to Bikini Bottom, where Mr. Krabs, the owner of popular fast food restaurant, the Krusty Krab, has a problem: a customer ordered a Krabby Patty with cheese, yet no cheese was put on the patty. Suddenly, SpongeBob SquarePants comes to the rescue. He has a brief chat with the customer, and with his briefcase full of gadgets, he takes out a pair of pliers and adds cheese, and the crisis is resolved. The whole scene reveals itself to be SpongeBob's dream.
Meanwhile, Mr. Krabs is preparing to celebrate the grand opening of the "Krusty Krab 2", his new restaurant. Hoping to become the new manager of the Krusty Krab 2, SpongeBob is completely convinced his name will be announced, since he had already been "Employee of the Month" 374 consecutive times.
Meanwhile, Plankton - arch-nemesis and business rival of Mr. Krabs who constantly wants to steal Mr. Krabs' formula of the Krabby Patty, is planning his ultimate plot - the dreaded Plan Z. At the celebration, SpongeBob's co-worker, Squidward, is given the manager title, as Mr. Krabs tells a heartbroken SpongeBob that he is just a kid and is unable to handle the task.
Meanwhile, Plankton arrives at the castle of King Neptune, who is prevented from declaring a ridiculous prison sentence by his intelligent teenage daughter, Princess Mindy. King Neptune is then horrified to discover that his crown is missing, having been stolen by Plankton.
SpongeBob arrives at Goofy Goober's Ice Cream Party Boat, a popular children's restaurant, to brood over his loss. His best friend Patrick arrives and joins him in a Triple Gooberberry Sunrise ice cream-eating spree, and SpongeBob experiences hangover-like symptoms the next morning. Meanwhile, King Neptune arrives at the Krusty Krab after receiving false evidence that Mr. Krabs had stolen his crown and sent it to the dreaded Shell City. Krabs pleads innocent, and King Neptune asks the crowd of onlookers if Krabs has a thieving nature. SpongeBob then arrives and insults Mr. Krabs out of spite, but after hearing the prospect of Mr. Krabs being executed, he and Patrick agree to travel to Shell City (where Plankton has sold the crown). Before departing, Mr. Krabs is frozen by King Neptune's trident, and Mindy warns the duo about the giant Cyclops guarding Shell City. She also gives SpongeBob and Patrick a magical bag of winds to return home with (a reference to the Odyssey).
With six days to retrieve the crown, SpongeBob and Patrick travel to a gas station next to the county line. There, their hamburger-like vehicle, the Patty Wagon, is quickly stolen by a mobster. One long walk later, they find it parked at The Thug Tug, a bar for tough, muscular fish. After a failed attempt to obtain the car's key, they begin to blow bubbles in the bar bathroom, which is a sign of weakness by the rules of the bar. A fin-fight as to who blew the bubbles results, allowing them to steal the key amidst the confusion and escape.
The following day, Squidward finds out about Plankton's plan and begins to tell on him by talking to King Neptune. Plankton begins controlling the minds of the townspeople through electronic bucket-shaped hats, disguised as free souvenir hats, ultimately taking over Bikini Bottom and re-naming it "Planktopolis." He also sends Dennis, a motorcycle-riding hitman, to eliminate SpongeBob and Patrick. Dennis is clearly an enemy of SpongeBob and Patrick. His name may also be a reference to Dennis Hopper's character in the movie Easy Rider.
SpongeBob and Patrick then obliviously drive into an area littered with piles of skulls and bones. Upon seeing a sign for free ice cream, Spongebob goes to get some for himself and Patrick, only to discover that the entire stand and the old lady managing it are all part of a frog fish's lure. Spongebob manages to escape it and gets into the Patty Wagon with Patrick, but the frog fish gives chase. At the last minute, upon approaching a monster-filled trench, the duo jump out, leaving the Patty Wagon to be eaten by the frog fish in midair (right above the trench). A few seconds later, a huge eel emerges from the trench and eats the frog fish.
Upon seeing the sheer depth and danger of the trench, though, SpongeBob gives up and accepts that he and Patrick are "just kids". However, Mindy arrives and shows them, via a magic clam, what Plankton has done to Bikini Bottom. When that fails to convince them, Mindy gives them fake mustaches in the form of seaweed, convincing them that they are now men. They pass through the trench without fear (singing "Now That We're Men"), and even befriend the various monsters that inhabit the trench. However, they are greeted on the other side by Dennis, who reveals that they are not really men (by ripping off their "mustaches") and is about to kill them (as per Plankton's instructions to "step on them") before being stepped on by a human scuba diver (the Cyclops), who takes SpongeBob and Patrick to the surface.
He takes them to Shell City, which is revealed to be a gift shop that sells knick-knacks made from ocean items such as shells, seahorses, and stars. SpongeBob and Patrick are put through a lethal drying-out process involving a heat lamp, but before dying, they realize that they made it to the crown after all, and shed two tears of joy which together form a droplet in the shape of a heart. As they slowly dry out, they sing the Goofy Goober song one last time, after which they completely dry out. However, the heart droplet slides down to the lamp's wire and short-circuits it, causing smoke to rise and activate the sprinkler system, reviving them and all of the fish-made knick-knacks, who lead an assault against the Cyclops. The duo takes the crown and flee, but Patrick accidentally opens the bag of winds without holding on to it, and it flies away. However, David Hasselhoff arrives and takes them across the ocean at sonic speed.
However, the cyclops' boot suddenly appears from the water, and brings an angry Dennis along with it. After several minutes of struggling, the angry assassin almost defeats Patrick and SpongeBob before being hit by an upcoming catamaran. Meanwhile, King Neptune has arrived at the Krusty Krab II to execute Mr. Krabs, as has Plankton (to watch). As Mindy desperately stalls for time, Spongebob and Patrick arrive over Bikini Bottom, and Hasselhoff opens his pectoral muscles and shoots the heroes into Bikini Bottom, deflecting King Neptune's execution beam with the crown in the knick of time (though burning Hasselhoff in the process though he survives). However, Plankton's hypnotized minions, which include King Neptune after Plankton jams a helmet on his head, attack the heroes, and as they are cornered, SpongeBob makes a speech about how being a kid is okay, as he did all the things everyone thought a kid couldn't do (i.e crossing the desert, defeating Dennis and the Cyclops, and returning the Crown) before pulling out a guitar and playing a rock version of the Goofy Goober song (which resembles the Twisted Sister song I Wanna Rock). SpongeBob destroys the mind-control buckets with the guitar and frees the citizens from Plankton's rule.
In the aftermath, Plankton is arrested, and King Neptune reaches an understanding with his daughter. He unfreezes Mr. Krabs, noting how he should be honored to have "a brave, courageous, and heroic young man" like SpongeBob. Realizing this, Mr. Krabs admits his past mistake and offers SpongeBob the managerial position. Squidward tries to downplay Krabs' offer, but SpongeBob leaps at the opportunity, and proclaims it to be "the greatest day of [his] life."
During the end credits, pictures are shown of SpongeBob's job as manager, who is seen happily mopping the floors, taking out the trash, sweeping the chimney, and getting a raise from Mr. Krabs (by only one penny).
Following the credits, a theater lady tells the pirates to leave.
SpongeBob and Patrick are in Jellyfish Fields blowing bubbles. Patrick tries to take pictures of the bubbles, but cannot as the camera is too slow. Patrick blames the camera and stomps on it, but SpongeBob says it is not the camera's fault, then accidentally blows a bubble and gets them both stuck inside it. SpongeBob and Patrick start screaming for help, unaware that the bubble has carried them into a cave, miles from Bikini Bottom. The bubble bursts on what appears to be half of the Atlantean Amulet. SpongeBob notices the letters "ANTIS" on the side. Patrick concludes that the amulet probably belonged to SpongeBob's ancestors, thinking their last name may have been "SquarePantis." They travel to the museum to find out what it is.
Later, Squidward, who had been visiting the museum at the time, accuses SpongeBob and Patrick of stealing the Atlantian Amulet as he saw the half SpongeBob was holding. He then realizes, as he sees that the amulet is still on its platform, that SpongeBob must have found the missing half, which had been lost for eons. Sandy, who was at the museum as well, says that when the two pieces are joined together, the path to Atlantis is revealed. As Squidward discusses that history of Atlantis, Mr. Krabs joins them, after performing a failed scam earlier, thus bringing the group together. Squidward joins the two halves, as they are all very eager to see Atlantis.
A van then falls from the sky, which is the key to Atlantis. However, the automated computer aboard says that "song fuel" is required in order for them to move. As everyone sings to make the bus move, they do not realize Plankton is on the bus, wanting to use Atlantis's superior weapons to become emperor of the city. Everybody sings about what they want to see in Atlantis, but this is ruined by Patrick, when he interrupts Squidward's musical number. They crash land in Atlantis on a topiary garden, and the king, Lord Royal Highness, gives them a tour of the Atlantian Empire. As they pass the door to the weapons arsenal, Plankton sneaks in and marvels at the hundreds of weapons. As they travel into the treasure, science, and art rooms, Mr. Krabs, Sandy, and Squidward respectively decide they want to stay in Atlantis as one room had more than anything they could ever get in Bikini Bottom. SpongeBob and Patrick, however, only wished to see the world's oldest bubble, which was kept safe in a glass container. Lord Royal Highness leaves them alone in the room so that he could prepare dinner for them. However, disaster strikes when Patrick takes a picture of the bubble and it pops. At dinner, SpongeBob and Patrick, terrified as to what will happen when Lord Royal Highness finds out, admit they popped the bubble, ready to receive their punishment.
Lord Royal Highness, on the other hand, is not mad and says that the bubble they popped was only a tourist attraction. He shows them the real deal, and Patrick takes a picture, thus popping the real bubble. The group is chased by the furious guards and LRH, when Plankton intervenes and tries to destroy them with a tank he found, which really only fires ice cream. LRH picks up Plankton, saying that a "talking spec" would make a much better replacement for the bubble. The group then goes back home and everyone except SpongeBob is crying; they want to stay in Atlantis.
SpongeBob wakes up and waves to the mailman. The mailman then crashes into a truck. SpongeBob hugs Gary and his shell explodes. He is beaten up by Gary and crashes into Patrick which ruins his mother's birthday cake. Then Patrick tells him "Idiotboy!" He then goes to Squidward's house and Squidward gets mad at him and yells "Idiotboy!". He goes to Sandy's Treedome, trips over a log and splashes the water in his fish bowl, which destroys the robot Sandy makes. She also then gets mad and yells "Idiotboy!". SpongeBob goes to the Krusty Krab, crashes into pots and pans, slips over water, which disturbs Mr. Krabs's moneydating. He goes to see what the racket is and lands in the french fry oil which burns the money he was dating. He gets mad at SpongeBob and says "IDIOTBOY!" He then thinks that he really is an idiotboy and sobs all the way home. Then he starts packing up his stuff and says goodbye. He passes the population sign and changes the number from 538 to 537. While on his way, he takes a nasty fall and bumps his head, causing him to developed amnesia. He wakes up in New Kelp City (a spoof of New York City), where bubble-blowing has been outlawed by a bunch of thugs. SpongeBob uses his bubble-blowing skills to run the thugs out of the city, and he is elected mayor for his actions. After a long period of not seeing him, Sandy, Patrick, Squidward, and Mr. Krabs go find him. When they found him, SpongeBob forgets about them thanks to the amnesia. Neither he can go home with his buddies nor stay in New Kelp City, where he is a hero to the citizens. Sandy hatches a plan. SpongeBob has amnesia, so if they bump him again, he goes back to normal. But now all the New Kelp City citizens have amnesia.
 Pages I Started
- The Patty Wagon
 Ideas For Episodes
(holding The Magic Pencil
), his General DoodlePat, and his army of doodled Bikini Bottomers
walk to Bikini Bottom
, ready for a WAR. Back in Bikini Bottom
, the News flashes all about the unwelcome guest. Also Squidward
owns the Krusty Krab
and the Chum Bucket
with an iron fist (Plankton
and Mr. Krabs
were taken by the Doodles). SpongeBob
500, Mr.Dr.Prof. Patrick
, New Gary
, Dr. Sandy Cheeks
, New Snellie
, Butterflyie (a.k.a. Wormy
, Mr. Squidward Tentacles
, and Spat
must stop the villains before it is to late. They have a dramatic battle that last 1 and a ½ hrs. (the movie is 3 hrs). The movie ends with DoodleBob
falling off the end of a mountain (with The Magic Pencil
), General DoodlePat and DoodleSuid running away for their lives, and the rest of the Doodles being captured. At the closing scene everybody left (SpongeBob
500, Mr.Dr.Prof. Patrick
, New Gary
, New Snellie
, Butterflyie (a.k.a. Wormy
), and Spat
) going to get some grub at the Krusty Krab
500 and Mr.Dr.Prof. Patrick
are talking about the battle and also Mr. Squidward Tentacles
gave the Krusty Krab
500). The credits have all of Patrick
's songs in the background.