In 1899, Mister Sinister awoke Apocalypse from his slumber once again, only to betray his master by infecting him with a techno-organic virus he had bred at Apocalypse's behest. As Apocalypse's ability to alter his molecular structure saved him, Mister Sinister fled while he could, driving his desire to find and create a powerful mutant to defeat Apocalypse later on. Sinister envisioned that the solution lay in Cyclops and Phoenix, the travellers he had met prior to his transformation. From his immense interest in their bloodline, he concluded that a Summers-Grey offspring would have the necessary power to overcome Apocalypse.
Mister Sinister kept doing his work all over the world. In 1907, one of his experiments, a polar bear, massacred the wolf pack that the clawed wild man known as Logan was living with in Canada. On the trail of Logan, Sinister sent his Marauders to finally hunt down his first mutant. As Logan was captured by a circus, Essex managed to vivisect and torment him, which led Logan to seek revenge. Mister Sinister was seemingly slaughtered by an angry Logan in his quarters. In 1909, Dr Essex resurfaced and joined the Ravencroft Institute staff, a good opportunity to have easy access to more subjects for his experiments. During this period, assisted by Victor Creed, Sinister got his hands on Logan again, lobotomizing and experimenting on him. Sinister's co-worker, Dr Claudia Russell, was able to free Logan, though she was killed by Sinister and used in his experiments. This was followed by Dr Essex leaving the institute.