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The Dark Design was a medical condition that certain Time Lords suffered from when they went mad. When this occured, the Time Lord begins to suffer from a storm across the surface of their brains. Those that suffer from this condition on Gallifrey were hidden away in institutions. (NA: Falls the Shadow)
Many inventive and genius Time Lords become corrupt and insane, which causes the condition of the Dark Design. Such as: Rassilon (BFA: Zagreus ), Omega (DW: The Three Doctors), Morbius (DW:The Brain of Morbius), Borusa (DW: The Five Doctors).
When Omega fought the Doctor in the anti-matter universe, he said he fought with the "dark side of his mind", and he was insane. So this may be the concept to having the Dark Design (DW: The Three Doctors).