Mister Sinister is one of three self-clones created by Nathaniel Essex, along with Doctor Stasis and Orbis Stellaris, as well as Mother Righteous, a clone of Essex's late wife, Rebecca. In many ways, he is the most similar to the original Essex, maintaining the Red Diamond on his forehead and the deep interest in mutants held by the original. Through the years, Mister Sinister became one of the greatest geneticists to have ever lived, skilled in cloning, creating new life, and even in the manipulation of mutant DNA for enhancing powers, incorporating mutant DNA to his own.
The original Nathaniel Essex had been transformed by the mutant known as Apocalypse, and the Mister Sinister clone spent most of his life scheming ways to break free from Apocalypse's grasp. For that purpose, he secretly manipulated the lives of major representatives of the mutant race, such as Cyclops, Jean Grey, Gambit, Havok, and even Professor X. The main results of his machinations were the creation of Madelyne Pryor and the birth of Nathan Summers, whom he believed to be the bringer of Apocalypse's end. Mister Sinister's actions directly crossed the lives of the X-Men after he ordered his Marauders to massacre the Morlocks.