(Aired on November 12, 1994)
The episode begins in the bathroom with Squishington 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.
Squishigton is ready to destroy his germ foe, but Germ Girl has a crush on Squish and wants him to chase her. Squishington pulls out a pair of metal tongs and charges at the germ, but his pit helmet falls overs his eyes and he can't see. Squishington ends up pinching Bumpy with the tongs, Bumpy thinks Squish wants a tickle fight and starts tickling him with the tongs. Bumpy tickles Squish and the two start laughing uncontrollably, Squish then decides to try another plan.
Later, Germ Girl is saying "he loves me, he loves me not" while picking at flower like germs. Bumpy and Squish are hiding behind some bushes pretending to talk with walky talkies. Bumpy traps Germ Girl in a sack, Squish then without knowing shoves Mr Bumpy in a sack and starts spraying him. Germ Girl is seen behind Squishy, Squish opens the sack and Bumpy is shown spitting out foam with blood shot eyes.
Bumpy and Squish start chasing Germ Girl through the jungle where she is cornered at the edge of a cliff, the boys charge at her but she splits in two, while the boys fall off the ledge. Squish and Bumpy crash land at the bottom of the cliff and Germ Girl appears, Squish thinks she wants to finish them off, but she says she surrenders to him.
Germ Girl talks about her desire for Squishington and says how much she wants him. Bumpy realizes that Germ Girl really like Squish and says she's not bad looking for a germ, Squishington on the other hand still hates germs and says they are evil and disgusting. While Squish is declaring his hatred for Germs, he brings the attention of a group of scary Purple Germs. The large Germs surround the two monsters and Bumpy realizes they are doomed.
The Purple Germs capture Mr Bumpy and Squish and tie them to stakes, the Leader of the Purple Germs accuses them of Microbocide and various other crimes. The Germ leader sentence the two monsters into a pit of the "Mother of all Microbes" where they would be devoured for eons.
Germ Girl stops the Purple Germ and stands up to him saying she is in love with Squishington (while he still doesn't love her back). The Purple Germ decide to let the prisoners go, if Squishington marries Germ Girl. Squish is reluctant, Bumpy tells Squish if he doesn't marry the "germ babe," they will be sentenced to death. Squishington still refuses and both Bumpy and Squish are thrown into a pit.
At the bottom of the pit, a giant Monster Microbe appears to devour Squish and Bumpy, they both start throwing stones at the creature and they see a clearly marked exit behind it. Bumpy tells Squish to talk to the Germ, Squish tries to politely reason with it, the plan fails and the Microbe tries to eat them. Bumpy distracts the creature with a card trick but it then eats his cards.
Mr Bumpy and Squish prepare for the end, but Germ Girl comes to the rescue armed with a disinfectant spray. Germ Girl tells the Microbe to stay back, she then sprays the creature causing it to flee. Bumpy cheers for Germ Girls bravery but it turns out that the spray also harmed her. Germ Girl is weakened and ask Squish if she could see him one last time.
Bumpy tells Squish it's time to get out, but Squish finally warms up to Germ Girl seeing that she loves him and cares for him. Bumpy tells Squish they are going to be eaten and reminds him he hate germs, but Squish doesn't want to leave Germ Girl.
The Microbe returns to finish them off, but Squish stands up to the beast and throws the spray bottle into it's mouth. The Microbe shrinks and is destroyed, Bumpy is astounded by Squishy's bravery. Squish says he usually doesn't approve of violence, but would do anything to save his friends from danger.
Later, the Leader of the Purple Germs congratulate Squish and Bumpy for their bravery and gives them both heroes medals. The two are dubbed great warriors and are granted their freedom. Germ Girl is upset that Squishington is leaving Microbia, Squish comforts the sad Germ and he finally feels the same way about her. Germ Girl and Squish both kiss and Bumpy blocks the screen saying "you can't do that on T.V".
Mr Bumpy and Squish both grow back to their original sizes and return to their world. Squishington tells Bumpy that he was wrong about germs, saying they are not all bad. Squish also says he learned a lot from Germ Girl and that he'll never forget her. Just then, Squishington starts to sneeze, his eyes go blood shot and his face is covered in pink itchy spots. Squish is sick and Bumpy teases him saying he has more than a memory from Germ Girl.
Squishington: Take That! And that! And how do you like That, germs! I’m going to clean you into oblivion! Zero tolerance wall to wall! Floor to ceiling! No place to run to baby! No place to hide!
Mr. Bumpy: Hiya Squish (gets squirted in the face)
Squishington: Surrender now germs, or face the wrath of my disinfectant! (gasp) Mr. Bumpy…. Did I disinfect you? I’m so sorry.
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!
Bumpy: This Microscope is out gateway to Microbia! Great googily moogily. You were right Squish, it really is a jungle down there!
Squish: See anything?
Bumpy: Nothing, except some Lions and Tigers… and some bears here.
Squish: Oh my.
Squish: A HA! Caught in the act of being a germ! What do you have to say for yourself.
Germ Girl: hmmm, what nice plasma you have stranger.
Bumpy: We are free! We are great! We are EPIC! Say chief, are these medals worth anything on the open market?
Germ Girl: (with a hanky) is it true what they say? You are leaving us?
Squish: I'm afraid so, don't cry. The petty problems of a monster and a germ don't amount to a pile of ooze in this crazy microscopic world. Maybe I'll have some sleepless nights but it will pass. Like a toilet flush in the wind...
Squishington: You know Mr Bumpy, I was all wrong about all germs being all bad. That germ girl sure taught me a lot . I’ll carry her memory wherever I go.... (Squish lets out a huge sloppy sneeze, his eyes become bloodshot and pink itchy spots cover his skin)
Mr Bumpy: (chuckling) Looks like you’ll be carrying more than a memory for a while.
- Mr Bumpy makes a reference to The Wizard of Oz when he mentions the "Lions and Tigers and Bears."
- In the scene where the Lead Purple Germ sentences Bumpy and Squish to their doom, the scene is a direct reference to Star Wars episode VI Return of the Jedi. For example the Germ says that he will be digested through out the eons while in Star Wars they said they will be digested for thousands of years. The pit also resembles the monster in the pit from Star Wars
- Goof: When Squishington goes up to Germ Girl, his hat is off his head and in the next scene Mr. Bumpy helps put the hat back on his head. When Squishington reply's "What do you have to say for yourself?" there is a hook on the left hand corner that was holding up the hat.
- Goof: During the scene when the Purple Germs award Bumpy and Squish as heroes, on the left side of the screen the background and the scenery is incomplete, clearly showing that the stop motion puppets are on a set.
- At the end of the episode, Squishington makes a reference to Casablanca, "The problems of three little people don't amount to a hill of beans in this crazy world."
- Germ Girl is voiced by Elizabeth Daily, who is also the voice of Buttercup from The Powerpuff Girls. Squishington's voice actor, Rob Paulsen also voiced Brick and Boomer the Rowdyruff Boys, and Bumpy's voice actor, Jim Cummings voiced the villain Fuzzy Lumpkins from the same show.
- Molly Coddle doesn't appear in this episode.