Yuggoth is a program created by Yamaki. It is designed to destroy a specific target.
Yamaki used it to destroy the digital zone in Now You See It, Now You Don't. He later used it on Musyamon twice, seemingly killing him the first time, but the second time Musyamon destroyed it.
Later, Yamaki sent Yuggoth after Pajiramon and Vajramon, but it disintegrated when it got near them.
During the battles with the D-Reaper, Yamaki equipped Grani with Yuggoth, enabling him to use Yuggoth Blaster, a powerful laser which destroyed the shield around the D-Reaper's brain.