Zelda Theories

The dark interloopers

It has been speculated by some that the Sheikah have some connection to the shadowy magicians known as the Dark Interlopers, the ancestors of the Twili that were banished to the Twilight Realm by the Golden Goddesses when they attempted conquest of the Sacred Realm.[3] The physical similarities between the two tribes have been noted, as the Dark Interlopers and the Twili both have the characteristic red eyes common amongst the Sheikah tribe and are skilled in "shadow magic", which was the forte of the Sheikah, who gained the title of the "Shadow Folk" due to this relationship to the element of shadows.

The eye symbol on the back of the Fused Shadow and above the throne of the Twilight Realm.
One piece of evidence highly cited by supporters of this theory is the presence of a similar Eye Symbol (somewhat akin to Agahnim's symbol) atop the throne of the Twilight Realm's ruler and on the back of the Fused Shadow, the weapon wielded by the Dark Interlopers during their conquest for power. Some even go so far as to suggest that the Dark Interlopers were in fact a sect of the Sheikah themselves, explaining their race's disappearance from Hyrule in one timeline and explaining why such a symbol would appear on the throne and on relics of the residents of the Twilight Realm. The fact that this symbol lacks the characteristic tear is also noted by theorists, who argue that this is perhaps the Sheikah emblem as it originally was and that those few that had not gone along with the Interlopers' schemes altered the symbol later to commemorate the sorrow they felt due to the actions of their comrades, though this is unconfirmed by any official source.
It has been noted by others that the Sheikah have often been portrayed as loyal servants of the Royal Family, in stark contrast to the Dark Interlopers, who let their greed corrupt their actions, thus complicating any theorized connection between the two. However, the Sheikah tribe's complete history is not known, leaving room for speculation as to whether they ever experimented with dark magic as did the Interlopers. While this is possible as nothing seemingly rules this out entirely, due to the incomplete information available about the tribe, it cannot be said with any degree of certainty whether or not the Sheikah took part in actions comparable to the Interlopers or had any dealings with them. Several other non-Sheikah villains like Vaati and Veran have also used Eye Symbols as well, leaving the question of a relationship to the Sheikah open to debate.