While his real name is unknown, it is revealed in "Consequences" that before Division he worked as an encrypter for the NSA. He also was illegally decrypting during which Percy then used to blackmail him. His death was faked and he was forced to work for Division.
In "Dark Matter" the Engineer comes to Division HQ to correct a problem with the Black Boxes. A wireless solution to the updating of the black boxes is designed by him and Birkhoff after which Percy kills the Engineer by breaking his neck.
Birkhoff is "promoted" and becomes the new Black Box Engineer.