SpongeBob and Patrick are in Jellyfish Fields blowing bubbles. Patrick tries to take pictures of the bubbles but they keep popping before the picture is taken. SpongeBob decides to blow a bubble that would last all day. SpongeBob blows a bubble that engulfs them both, and carries them into a nearby cave. The bubble suddenly pops as it makes impact with an ancient piece of gold. Eager to discover what exactly it is, they take it to the Bikini Bottom Museum where they (literally) run into Squidward. At first, Squidward thinks that SpongeBob and Patrick were planning on stealing the first half of the amulet which is housed in the museum, but upon attempting to return it to its spot realizes that what Patrick and SpongeBob had was in fact the missing half. At this point, both Mr Krabs and Sandy join them. The pieces of gold are then reunited which summons a luxurious bus (or 'van' as Squidward calls it) piloted by a robot and fueled by "song." During the song to fuel the bus, it is revealed that Plankton has stowed away in a compartment at the front of the bus and plans to control the lost weapons of Atlantis. Once they arrive there,(accidentally crash-landing in a topiary garden) they meet Lord Royal Highness who shows them the riches, knowledge, and art of Atlantis. Meanwhile, Plankton escapes from the compartment and sneaks into the vault storing the weapons. After looking around at the weapons, he chooses to commandeer a tank (seemingly at random) to start off his diabolical scheme. While this is happening, Mr. Krabs enjoys the money vault, Sandy enjoys the science lab, and Squidward enjoys the hall of art (the rooms each had been planning to see). In the money vault, money, gold, and prized objects are found and mostly stashed in Mr. Krabs's pants pockets. In the science lab, Sandy enjoys the devices, a biomass converting device that turns any household object into ice cream (a bug the Atlanteans haven't worked out), a germ-fighting, interactive, micro video game, and makes an automatic feeding device. And in the Hall of Arts, Squidward journeys through paintings, gets modeled by artmakers, and even makes his own painting, claiming to have learned more about art in his short time in Atlantis than he did while at college. But everything goes wrong when SpongeBob and Patrick are left alone with the World's Oldest Living Bubble. The flash from Patrick's camera when he takes a picture of themselves with the bubble causes it to burst, and the pair go to dinner and insist on leaving. When Patrick reveals their mistake, Lord Royal Highness tells them that the bubble they popped was a prop, but when he shows them the real bubble, Patrick takes a picture of it and it also pops. The Atlantean is furious and summons the Royal Guard to seize the gang, but Plankton appears. He fires the tank at SpongeBob, the gang, and the Atlantean Royal Guard, but is foiled when it is revealed that the weapon he had chosen only shoots ice cream. He jumps out of the tank and in frustration kicks it, injuring himself. However, Lord Royal Highness seems delighted - a talking speck will make a great replacement for the bubble. Finally, the Atlantean king loads SpongeBob and his friends back onto the bus and removes the amulet, giving it to one of his soldiers to dispose of to ensure no more "visitors like these". SpongeBob is the only one eager to return to Bikini Bottom, and he sings of his delight in returning home as everyone else cries in protest.
Patchy is stuck in traffic at Encino, California. Then, his cell phone rings, and Potty warns that he's going to miss the movie. Patchy yells at the guy driving behind him for honking at him because he is trying to talk to his parrot. Patchy tells Potty to record the movie, but Potty tells him that he threw the videotape in the trash, making him mad. Then, the traffic lines moves, but suddenly, he finds himself nowhere, and yells out "Encino, it's gone.......NOOOOOO!" Then, he cries that this isn't the only time a Lost-City had occurred. Then, he tells us that the episode is what we should watch instead of watching him suffer. Then, Patchy gets his radio fixed, but not for long when it explodes again and produces smoke. Patchy later gets the hallucinations, and he finds a boy dressed in a tall sponge outfit who cries out that he is SpongeBob in real-life form. Then, Potty wakes him up after he thought he is back in Encino, which is all just a dream. Patchy begins to eat a sandwich, but he finds mayonnaise on it. After this, he finds Three Aliens and the portrayal of Encino. The Three Aliens explain that their son Norbluckfive was playing with his Shrink-A-Tron again. Patchy yells at them that he wants his town back in full size, and he keeps saying There's no place like home!. Sympathetic by Patchy's crying that he wants to go home because he missed the entire story, Norbluckfive's mother gets the Shrink-A-Tron given from her son, and she presses the big red button control, making a tornado disaster to fix it up. Then, Patchy is glad to be back in Encino, but soon, a giant Potty the Parrot crushes him into the house, realizing that now he is shrunk into Encino, not that Encino became bigger.
Squidward: You boobs found the missing half of the Atlantean amulet!?
SpongeBob: What's an Atlantean Omelet?
Squidward: Amulet! Not omelet! It's the key to untold riches!
Mr. Krabs: Did somebody say untold riches?
One of the paintings in the museum in the background is "The Scream" but instead of a man, it is a fish.
In the videogame "Mission Start: The Germ Warrior", you can see a code that says 1991 @ Nickelodeon Inc., an Entertainment Rights group company. The title screen (and title) are most likely a parody of Street Fighter II: The World Warrior.
Germ Warrior is a parody to the Classic Mario Bros.
Sometimes, in Indonesia they cut ALL the songs, Sometimes they didn't.
When everyone is in the video game, it says Nickelodeon at the bottom. It also says the game was published in 1991 (debut of Nick's first Nicktoons: Doug, Rugrats and Ren & Stimpy). This was the second time it was used, the first time was in Have You Seen This Snail?
When the fanfare plays during when SpongeBob and friends arrive at Atlantis, LRH falls which is like Willy Wonka and the Chocolate Factory (1971) when The golden ticket winners arrive at the Chocolate Factory and he falls.
Mr. Krabs' "I Hate Mondays" Shirt is a reference to Garfield the Cat's catchphrase
Many fans complained that there was a lot of talk of this episode being "The first ever SpongeBob tv movie", because it was only 45 minutes long.
In the original airing, only the SpongeBob plot was aired, all subsequent airings show the Patchy plot, alongside the SpongeBob plot
The following enemies working for Bowser the koopa king. **Wiggler (The yellow caterpillar.) **Spiny (The red shelled creature.) **Chain Chomp (The blue ball creature who acts like a dog.) **Goomba (The brown-and-yellow mushroom creature.) Bowser and the other aforementioned creatures all happen to be the main villains of the Mario video game series created by Nintendo. In fact, during the "Germ Warrior" scene, Sandy uses a warp pipe, another recurring element from the Mario series.
Also, the part where LRH throws Squidward into the painting might be a reference to a popular Mario game, Super Mario 64, where Mario has the ability to jump into levels via enchanted paintings.
Patchy mentions he is stuck in traffic on US 101. US 101 really does pass through Encino and is a major commuter route for drivers going to or from Los Angelas.
In the Video Game Version of this Episode, Mr Krabs has no lines.
The scene where Sandy fights the germs is a reference to Dr. Mario.
On the premiere of this episode, Patchy was seen at Atlantis in Paradise Island, Bahamas. This wasn't shown on later showings.
The way Sandy warps into the video game is similar to the way some of the characters in the Mega man franchise of video games enter or exit levels.
The story board showed Patrick eating the old living bubble, but it was changed by taking a picture of it and pops.
If you hear a noise when Sandy shows her invention to LRH, it her stomach growling.
LRH is voiced by David Bowie, yet he does not have a musical number in this episode.
The Video Game of this episode is the only Spongebob game produced for the Playstation 3.
Running Gag: Whenever Patrick takes a picture of the bubble it pops.
The "I'll destroy all of you!" quote Plankton said was also used in the SpongeBob SquarePants Movie.
After the episode during the credits, its song is extended.
The premiere of the special drew 8.8 viewers, the highest audience in the history of the show.
The citizens of Atlantis bear a striking resemblance to the Blue Meanies from Yellow Submarine.
Under the title , Germ Warrior, you can see the Nickelodeon logo for the second time. The first time was in Have You Seen This Snail? where it's found in the paddle ball box.
Canned bread makes its 2nd debut as part of Squidward's Dali style painting.
A scene of Squidward in one of the pictures is the painting from the movie "Looney Tunes:Back In Action!"