(Aired on November 11, 1995)
The episode begins with the same opening as "Adventures in Microbia", Squishington is shown in the bathroom and on a cleaning spree, he goes over the top with cleaning as if it is a battle.
After cleaning the floor, he climbs over the walls and starts cleaning the ceiling. Squish then starts wiping the sink, Mr. Bumpy says hello to his friend, but Squishington squirts him on the nose with disinfectant. Mr Bumpy taste the foam on his nose and licks it off with his tongue, but then spits it out.
Squishington has a great hatred of germs and Mr Bumpy tells him that he must face the germs "face to protoplasm". Bumpy finds a microscope and says it is literally a jungle down there. Squishington is prepared to battle the germs and the two are instantly shrunk to microscopic size. The two monsters, leap down the microscope and enter the world of Microbia.
Soon the two monsters are shown searching for germs, Squishington ask Bumpy if he can see anything through the binoculars and Bumpy responds he doesn't see anything except for some lions, tigers and bears. Squish then says that the germs must be hiding because they are afraid of the big bacteria hunter. Suddenly Squish hears something and quickly grabs the binoculars from Bumpy, while the binocular strap is still around Bumpy's eye stalks and hurting him.
Squishington looks through the binoculars and examines the area, soon he discovers a group of large scary Purple Germs gathering around and talking with each other. Squishington sees the germs then screams and runs away like a coward. Bumpy still has the binocular strap around his eyes and is being pulled by Squish, Bumpy tries pulling back on the strap and he reminds Squish that they are trying to hut the germ menace. Squishington pauses and realizes this, he comes to his senses and returns.
Squish then grabs the binoculars again much to the dismay of Mr. Bumpy, Squish observes the Purple Germs and mutters that "they don't look very neat and clean." The Purple Germs hears this and say they don't care about clean, the sinister sharp tooth germs then walk up to the two monsters and surround them.
The Germs ask why do they need to be neat and clean for, the germs say that they are smart. Germ Girl appears and says that they have "kind hearts", the Germs then says that "so what if they smell like", Squishington quickly interrupts the Germs before they can say the finishing rhyme, his pit helmet flies into the air and hits Bumpy on the head. Squishington then rushes up to the germs and decides he wants to explain to them through song.
Squishington begins to sing slowly and says that it is good to be smart and to have a kind heart but he tells the germs that there is something else they can be. Just then the tempo speeds up into an upbeat gospel style music number and Squishington begins to sing "Neat and Clean (Song)".
Then Squishington gives out towels for the Germs and continues to sing the song. Squishington then says to pick up a mop and clean up every speck and drop and says that it is important to be "Neat and Clean". Squish then calls out for Molly Coddle and she joins in and sings about picking up a broom, cleaning up the room and sweeping away the gloom and both Squishington and Molly sing together in the chorus.
Then Destructo appears to sing his own verse and tells them to pick the stuff off the floor and putting in it a drawer. The Germs enjoy the fun song and begin to dance along with their towels. Eventually, Mr. Bumpy gets swept up in the song and says to pick up the socks and to put them in a box, but becomes shocked when he realizes that he his singing about being clean and he is usually against hygiene. Then both Squishy and Molly sing together chorus the second time while Bumpy says he didn't mean singing about being clean.
Then the Cute Dolls starts to sing there own verses about picking up your spray and squirting your worries away and the second doll sings about wiping clouds of gray and about being neat and clean. Then Squishy and Molly sing the chorus the third time and one of the Cute Dolls says it's because chic magazine, Squishy cuts in with "Says" and both him and Molly sing about being them being neat and clean.
Squishy then says that the Germs can take it from him and that there is just one thing to be and shows his philosophy and that they gotta be neat and clean. Squishy tells everyone to sing then Squishy and Molly sing the chorus the fourth time, Squishy mentions if you are a king and Molly mentions or if there a queen and one Cute Doll mentions about a being a big strong machine and Destructo mentions about how they "gotta be neat and clean". Squishy then tells everyone to sing one more time, then Squishy and Molly sing the chorus the fifth time and Bumpy mentions about if they play a tambourine, and Molly and Squishy sing the chorus one more time and everyone cheers as the song ends.
Then the Germs and Germ Girl start chanting about being neat and clean, Squishy tells Bumpy how they finally got through to them and Bumpy agrees and then mentions that there still germs and that they still came to stop them. Squishy and Bumpy wink to each other and turns on the germs and spray the Germs and Germ Girl with the disinfectant spray. However instead of being harmed by it, Germ Girl and the Germs enjoy it while Bumpy and Squishy sing the reprise of Neat and Clean (song) and the episode ends.
- This episode has the same opening as the season 1 episode, Adventures In Microbia. However, changes have been made to the main plot and the musical number takes up the rest of the story.
- Squishington's line "no where to run to baby, no where to hide" was repeated twice in the episode.
- Goof: The Lead Purple Germ speaks two different lines of dialogue but two different voices come out of the one character. This is an error that is often happens in animation when they have similar looking characters with different voices and the animators get the dialogue mixed up.
- Goof: When Mr Bumpy puts the hat back on Squishy's head, there is a hook on the left side of the screen holding up the hat. This footage was also used in "Adventures in Microbia."
- The Germs were about to make a flatulence joke, but Squishington quickly stops them before they can say the finishing word.
- During the song there is an innuendo in one of the lyrics, Squishington says that the "pleasure never stops" and it shows footage of Squish playing with a rubber duck and squeezing it below off screen. The scene zooms out and Squish lifts up the rubber duck revealing it. This joke mostly goes over the young viewers heads.
- During the song "Neat and Clean", Molly Coddle sings along with Squishington. Destructo and the Cute Dolls also appear during the song even though it doesn't explain how they got to Microbia.
- In Adventures In Microbia, Germ Girl was harmed by the disinfectant spray while in this episode, Germ Girl and the Purple Germs enjoy the foamy spray.
Mr Bumpy: Getting a little carried away with the cleaning, huh Squish?
Squishington: I am at my oozes end. I clean with extreme prejudice but they just keep coming!
Squishington: Hmm... They certainly don't look very neat and clean.... (watching the germs through the binoculars)
Purple Germ: Clean Shmean! We're Germs for crying out loud! (the germs surround Bumpy and Squishy)
Purple Germ: Yeah, why do we wanna be "Neat and Clean" for? We're smart.
Germ Girl: We got kind hearts...
Purple Germ: So what if we kinda smell like-
Squishington: Wait! Let me explain it to you through the wonderful medium of song....