Emily Spencer left Nathan Spencer an unknown time before he became a Bionic Commando, but a few years before he defeated Master-D. They married as soon as they met, but Nathan signed up for the Army and soon left Emily. It was years after Spencer and other Bionics got betrayed that he learned the truth. Nathan was tricked into service by Super Joe who had information on Emily's disappearance. Later, Spencer found out that Emily had been with him the whole time. In order to achieve an operational status, people close to the Bionics user must undergo an unexplained process, where they become a part of the Bionic part. It's never explained what part of Emily is in the arm, and if the rest of her is alive or in what condition. With the failure of the 2009 game and closure of the developers, it's unlikely that fans will find out which plot lines started by the studio will be tied up.