After William Birkin transferred to the Raccoon City underground laboratory, John replaced him as senior researcher at the Arklay laboratory, and took over the B.O.W. (Bio-Organic Weapon) research project.
Although he was a gifted scientist, the inhumanity of his research took its toll and he began to shun his superiors. He would find some solace in his girlfriend Ada Wong. In the end John would ironically fall victim to the T-Virus.