The Evolutionary Experimentation Program (EEP) was an experiment run in Vault 87 on the orders of the United States government to create improved soldiers for the American military. Unknown to their fellow Vault dwellers, some inhabitants of the Vault were subjected to the experiments. Although reportedly having died from an "unknown cause of death," they were in fact exposed to a genetically-modified version of the FEV virus.
After their infection, the subjects underwent physical and mental changes over a period of about 2 weeks. Their form became asexual (genderless), more muscular, and their skin toughened. However, their mental abilities diminished and they became overly aggressive. They became the super mutants found on the East Coast in the Capital Wasteland. The mutants found in Vault 87 mention that they capture humans and dunk them in vats filled with the green nutrient solution that feeds the FEV to make more super mutants, continuing the program.
This particular incarnation of FEV produced super mutants slightly different than their west coast brethren seen in the earlier Fallouts. Generally, they are dumber and more hostile. However, the EEP mutants have a healthier appearance; West Coast mutants often have erratic mutations, like blisters and deformed body parts.
Fawkes was presumably a victim of this program. Despite the fact that FEV exposure made him lose nearly all his memory of a human life, he talks about how familiar Vault 87 feels to him. However, he somehow retained some intelligence as well as his system of morals through the transformation, and in fact gained a wealth of knowledge from the computer terminal in the room to which he was confined after the other super mutants discovered his "defect." Also, he is wearing a torn-up Vault 87 jumpsuit, which he either found or is a semblance of his previous life within the vault as one of its former human residents.