The Brotherhood of Shadows are an unholy, fanatic cult based around the demon sorcerer Quan Chi and forever worship the fallen Elder God Shinnok. Its countless members are ever scheming and planning for his release from the Netherealm. Its trademarks are stealth, secrecy, deception, and its involvement are with black magic and necromancy. They achieved their goal when Quan Chi was able to get hold of the sacred amulet needed to free Shinnok from his eternal prison, from where he already controlled the entire Netherealm. Agents such as Noob Saibot and Reiko rose to prominence during the subsequent war with Princess Kitana and the people of Edenia, Raiden and his Earthrealm warriors during the events of Mortal Kombat 4.
Their joint effort ultimately failed and Shinnok was defeated. In the events leading up to Mortal Kombat: Deadly Alliance and Deception, Noob Saibot began eluding Quan Chi's control and prepared for the creation of his own armies, while Sareena and Ashrah left the Brotherhood. With Shinnok eliminated as a presence to be reckon with and Quan Chi's own plans with the Deadly Alliance, the Brotherhood seems to have lost its importance or is on hold. It appears that for most (former) members, their time spent with the Brotherhood was merely a catalyst for more important things to come. It was later revealed in Mortal Kombat: Armageddon that Sareena is again working with The Brotherhood of Shadow under Quan Chi's spell. This story is also revealed through her newly released bio. Noob Saibot also led the brotherhood of shadow to the Lin Kuei palace to overthrow his brother Sub-Zero as well as convert his ninjas into cyborg demons.
At the heart of the Brotherhood of Shadows' fanatical religion is these diabolical zealots' very desire to bring about the day when the malevolent Elder God Shinnok is finally and completely set free from the dark depths of the Netherrealm, and his will is done. And they'll soon stop at nothing to achieve their insidious, utopian dream of being at the right hand of their divine master and creator, and thus forever rule all creation itself.