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A Spore is a fungus created by Cobra-La that is designed to literally and brutally mutate the entire human race into "mindless beasts" as eloquently put by Pythona. It is a brownish colored fungal spore that was launched by Spore Launchers into outer space, so that they can, when energized by the Broadcast Energy Transmitter, mature and infect the entire human race as they rain back down to Earth.
Appearantly, the spore works by destroying the human brain, mainly the cerebrum,leaving what is left of the brain intact, in which then people become animalistic. The spore was also intended to float about long enough to render any people born after the contamination to also have their brains destroyed by the spores. It may have been possible that after the fungus matures in the destroyed areas of the brain, further spores may have been depicted as being exhaled back into the air to keep the destructive cycle going forever as long there are humans on Earth. In the case of Cobra Commander, since he was a Cobra-La operative, the spores turned him into a snake , and he went insane as the spores destroyed his brain. (He kept repeating, "I was a man. Men may rule, not snakes. I was a man." as the spores destroyed his brain and mutated his DNA into that of a snake) The spores were also mutagenic, evidenced by a comment made by Zarana to a Drednock("Seal this up, (to keep the spores out) unless YOU want to wake up as a CLAM or something.")
Fortunately, these were destroyed by Lieutenant Falcon when he caused the "BET" to overload and burn up the spores, and as the remains came back down, atmospheric heating (this is how you see a meteor) burned out the remains.