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The Recess Gang is in science class where they witness the binary fission of a bacterium. Rus is horrified when he finds out that bacteria and germs are the same thing, and believes that all germs can cause decay and disease. Mickey begs to differ, saying that bacteria and germs are living creatures and even gives each germ an individual name. As Mickey is about to release the germs, Greta makes the problem worse by informing Rus that germs are everywhere, causing him to run out of the classroom in a panic.

In the boys' room, the paranoid Rus is shown cleaning himself. At Recess, he shows up wearing a biohazard suit protecting him from germs. C.J. now realizes that Rus is overreacting, as Greta tries to clear up a few misconceptions, before suddenly starting to feel ill; she has caught a cold. It concerns Rus who is convinced that the germs have made her sick.

Rus is wandering round the playground in his suit, spreading the word about germs, frightening the Megans and even frightening the Aubrees, when Brinklow arrives, agreeing to help Rus in his anti-germ campaign, and putting on his own biohazard suit.

Rus holds a meeting in the playground discussing the dangers of germs, which Mickey observes atop Old Crusty. With nearly all the students joining Rus' campaign, Mickey decides to speak out for germs, but is jeered at by the students. Soon enough, they are cleaning up the playground and wearing masks and surgical gloves, and a couple of tanker trucks arrive to disinfect the area of germs. Mickey decides to protest by holding up degermification, and refuses to budge. This only leads to a furious tussle between the two, which results in Mickey dropping his slide and breaking it. Believing that Rus killed the germs, Mickey becomes furious with him and the two start a big fight, which continues for some time until Greta arrives, having recovered from her cold.

Greta rekindles Rus and Mickey's friendship by saying that 1) they are both behaving ridiculously; 2) Rus was wrong to try to disinfect the world just on account of her having taken ill because germs are everywhere, and one must learn to live with them; 3) Mickey was wrong to act like germs are his pets because they are single-celled and therefore have no legs, eyes, or even brains; 4) germs are neither good nor bad and they are just a part of life; and 5) while germs did make her sick, germs also made her healthy again; specifically, antibiotics are germs that help the body fight illnesses. She then mentions some germs are for making medicine, yogurt, and (this is to Rus and Mickey's major enjoyment) cheese. Rus and Mickey both make up for earlier, and Rus happily re-opens the playground. The disinfectant crew then depart, and the gang plays ball.