The episode opens with Stinky, Gerald, and Arnold watching Sid catch frogs. They are preparing for the upcoming Frog Catching competition. Stinky is worried that they will lose the competition because Wolfgang is entering a team. Arnold tells Stinky that there's nothing to worry about because Sid is the best frog catcher. Sid is able to catch frogs in his mouth, a practice which disgusts the others. He tells them that it's not gross and shows them Sidney, who is the first frog he ever caught.
The next day at school, they watch a hygiene video about germs. Sid is freaked out by the video becoming a germaphobe. He starts with a can of disinfectant and gloves, then he throws away Harold's lunch and then returning home to obsessively clean his room and covering everything in plastic bags. He goes to school the next day in a diving suit and gives Arnold Sidney, telling Arnold that Sidney is too germy to keep. Helga claps some erasers in Harold's face who then sneezes on Sid's helmet. Sid freaks out and returns home.
Arnold goes to Sid's after school to give him his homework. Sid is still obsessively cleaning his room at this point. Arnold tells Sid that there are germs everywhere and he just has to accept it which results in Sid panicking. Sid has a nightmare where he is controlled by the germs like a puppet and being swarmed and eventually eaten by giant cockroaches (the man from the hygeine film also appears and becomes one of the roaches as well). He wakes up the next morning and hears Sidney croaking outside the door. Sid opens the door and sees Sidney looking up at him. Sid cries, and picks up Sidney exclaiming that he's back.
At the competition, Gerald has given up all hope of winning the competition saying that Sid was their only hope. Sid then shows up beating on his chest. With Sid's help, the fourth graders of P.S. 118 win the competition. Afterwards, Stinky comments about Sid's drastic change. Sid says that it's all a part of life. It's just nature and he wouldn't want to give up something as big apart of his life as Sidney is. After Sid kisses Sidney, he jumps on Helga's head who screams in panic and then jumps in a body of water. Sid says, "What's bugging her?"