The Commander grew up with his family on the Space Colony ARK, and was a good friend of Maria Robotnik. However, he saw Shadow being created by Black Doom and Gerald, and his family and Maria were killed in the GUN military's attack. He harbours a deep personal hatred towards Shadow the Hedgehog, blaming him for their deaths, and sends his forces to destroy him throughout the game. The Commander appears to have heterochromia, as he has one blue and one amber eye.
After Shadow defeats Devil Doom and destroys the Black Comet, The President states how ironic it was that people treated Gerald like he was evil, and he ended up saving them all in the end. The Commander and the President realize they were wrong about Gerald's intentions and that he was truly a good hearted person. They decide they will help create peace for the world in honor of Gerald and his memory. In the Expert Mode, it is revealed that the Commander had become a grandfather one week after the events of Shadow the Hedgehog and invited Shadow over as part of his apology to the Hedgehog after realizeing that Shadow is not evil but a good harted being (It is assumed that this was when Shadow became an agent of G.U.N. and accept humanity.)