Kokuu Hyouryuu Nirgends (1996)

Basically, it alternates between the adventure part, which depicts the interaction with fellow crew members, and the battle part, which controls the humanoid deformable fighter Grywurm (Glühwurm) and shoots down enemy planes. It's easy to imagine a flight simulator or a 3D shooter as a fighter, but in reality it's a command line plus real-time. The depiction is 3D, but PC-FX does not have polygon function, so it is represented by sprites used in FC and SFC and pseudo 3D expressed in BG.