The Shadow Plague was an illness that plagued the island of Mata Nui prior to the coming of the Toa Mata. It was caused by Makuta Teridax, spreading the essence of Shadow Kraata as an airborne virus. All Matoran affected by the disease fell under the control of the Makuta.
However, he eventually gave up on the project when he noticed that the effects were only temporary, unlike infecting a Matoran's mask. There were also too few Shadow Kraata for the idea to be practical anyway.
Eventually, the disease faded away and the Matoran affected by it recovered, but the six Koro were still damaged and took years to repair.