Shinnok formed the Brotherhood of the Shadow after he acquired control of the Netherrealm from Lucifer. By aiding Shinnok, Quan Chi was made leader of this group. The Brotherhood were Shinnok's personal protectors, spies, and assassins.

After Shinnok's failed attempt to invade Edenia during the event's of Mortal Kombat 4, the Brotherhood's presence began to fade. High ranking members, such as Reiko and Noob Saibot, began to separate themselves from the clan. At this time, the status of the Brotherhood of the Shadow is unknown.