As noded by discofever in the Knowing is half the battle! node, "The Germ" was by far one of the coolest G.I. Joe episodes ever.

Despite the warnings from a benevolent research scientist, Agent X-99 steals "Bacteria X" from a science lab and returns it to Destro. After Destro announces out loud his plans to take over the world with it, the Crimson Guard come in and take the vial away from him... as well as a vial labelled "Experimental Growth Serum". When Destro sends his generic blue Cobra troops to get back the vials, a fight ensues that results in the two vials crashes and mixing. From the primordial stew, a giant purple germ appears and begin crawling away, growing larger as it eats everything in its path. It eats the Cobra base and continues on.

Enter the Joes. With the usual chant of "Yo Joe!", they take to sky and start firing pesticide filled missiles at the germ, which is now tredging its way across farmland. Rather than destroy the germ, the missiles are absorbed and spit back out at the Joes. The planes that aren't shot down skywrite a message for everyone to flee their homes. A farmer and his wife run out of the house as the germ absorbs it, with the farmer cursing his wife for making her "surprise stew" again.

Meanwhile, Airtight has been developing a plan to detonate an antibiotic bomb inside the germ. The scientist who created the germ warns the Joes that an antibiotic will not work, but Airtight has lost radio contact inside the germ. Of course in typical G.I. Joe fashion, although the germ eats everything, nothing is actually destroyed, or anyone killed, so Airtight meets up with a bunch of Cobra guards is scuba gear. After a brief fight, he detonates the bomb and exits the germ.

But the germ isn't destroyed! Instead, it undergoes mitosis (how's that for teaching science to third graders). Splitting in two, one germ continues on. The other heads for New York City. Of all people, Shipwreck decides that the best solution is to sugar coat the medicine to make it go down easier. The scientist suggests that apples, in sufficient quantities, have enough poison in them to kill. The Joes go to work.

The first germ is eradicated quite easily. The Joes simply fire herd it into an apple orchard by firing missiles near the germ's path. The second one doesn't die so easily...

Cover Girl and Shipwreck lead the Joes in the second battle, as they load tanks, portable cannons, and ships full of apples. As the germ approaches New York City, the Joes open up, apple-bombing the fuck out of the germ. Shipwreck stands just feet in front of the germ lobbing apples into it by hand. At the last moment, Shipwreck and the gang lunge into the water. Meanwhile Ace and his Skystriker team apple bomb the germ from above, finally killing it, and splattering germ residue all over the rest of the Joes.

When the germ spits out two of the Cobra troops who were inside it, the gang makes some clever anti-Cobra joke. Everyone laughs, and they cut to the public service announcement.