This episode starts out with aliens in their spaceship attacking the town, and a scientist asking what they were going to do. In the middle of the conversation, a woman clears her throat and shows an alien in a glass tank. The woman said she was going to make a demonstration, and pulled out a pepper shaker. One of the scientist said that they will destroy them with pepper, but he was wrong. She took the pepper, sniffed it, and sneezed into a tube that led into the tank on the alien, and the alien exploded. She tells them that the aliens are allergic to germs. So they cut to a scene where american soldiers come to the aliens and sneeze on them, defeating this. This is only a show, that GIR is watching on TV with Zim. GIR screams Hooray for Earth, and Zim tells him that Earth is their enemy. Zim laughs at the idea that the alien race could be defeated by something as simple as germs, and Zim runs to his lab. He checks with the computer, and the computer tells him that many an alien has been horded off by germs, and that he should be prepared with a pair of germ spying micro-goggles. Zim presses a button for a free five second demo, and looks around his lab to see that it is full of germs. The trial is over and Zim is freaked out. He orders the full version.
The goggles are sent to the door, and Zim picks up the package carefully with napkins. Zim puts on the googles, looks around, and freaks out again. He runs into the kitchen. Just then GIR walks in the front door holding a muddy pig over his head. He tells him that they are going to his room. Zim run in the living room with a mop, and some disinfectant. Zim starts cleaning.
Zim is finally done, showing the house through is germ goggles. There is only one single germ that is left, and Zim sprays it three times to kill it. GIR walks in, telling the pig bye as it drives away, turns to look at Zim, and germs start spreading everywhere. He says that he is going to roll around in the floor a bit, and after a while Zim tells GIR to stop, that he's disgusting. GIR tells Zim that he needs a hug, and the germ infested GIR walks toward Zim. Zim runs out the house screaming. He turns around to look at the house, and starts screaming even more, and sprays everything. He quickly gets back inside, and GIR tells Zim he's gonna hug him. Outside, one of the lawn gnomes disappears and a tree appears with GIR tied to it. GIR starts to run around, and gets choked as the rope gets tangled.
Inside Zim's lab, Zim is going crazy spraying everything. He starts talking to himself about how he is failing to see the bigger picture of the mission, and that the germs must not get in his way. He also starts thinking about how the kids at skool will alarmed, as well as the tallests. Zim reports to the tallests. Before he comes on the screen, they talk to each other how they should've got him a mission on the sun or a planet of broken glass, or the exploding head planet. Zim comes on and starts to report, but he is interrupted due to many germ sitings. Zim finally runs out of disinfectant, and starts screaming that he will destroy all the germs, and the picture fails out. Unaware of whats going on, the tallest ask each other if that scared them too.
Outside, GIR is still running around on the rope. Zim comes outside to tell GIR that he is out of disinfectant, and that he needs to go to the store to get some more cleaning things, and wants GIR to come with him to help carry stuff.
They finally get to the store, and Zim is stopping to spray things. GIR gets aggrivated and steals the spray, saying that he wants to try, when GIR is distracted by MacMeaties. GIR runs towards it with the can still in his hand, and Zim starts to chase after him. Zim comes in and starts to get afraid by the germ infested people. He finally runs into GIR and asks where the disinfectant is, and GIR says that he lost it, pulls out a hamburger, and asks if he wants a bite. Zim starts to get afraid, but notices that the burgers are completely germ free. He goes up to the cashier (and calls him burger lord, lol) and asks how the burgers are completely germ free. The man gives a history about how NASA launched a space shuttle in search for the space meat that is completely germ free for the astronauts, and how the scientists have had even more advances in the space meat, and how seeing it as an oppertunity for the MacMeaties corporation not be sued by angry customers being poisoned by their regular meat, they decided to use the space meat. Zim tells the man to give him all the meat.
The next day at school, Zim comes in all dressed in meat.