The Terran Confederation military is divided into three branches: Navy (starship crew), Space Force (most of the pilots) and Marines. Officers are allowed to transfer between branches, thus explaining Christopher Blair's new rank of Commodore (before, he was a Space Force Colonel).
Designed as a bridge between the Blair/Kilrathi-centric earlier Wing Commander games and a Casey/Insect-centric Wing Commander. The demise of Origin, however, implies that this was the end of the Wing Commander universe.