Years of conflict have finally mellowed mankind. The super soldier war brought nothing but destruction, the bio-chem war was a failure and a mess, and in a time of peace, a new war brews on the horizon. In their most difficult struggle yet, mankind must draw upon tactics from every war and face a new threat together or risk destruction.
An unforeseen enemy prophesizes the death of mankind...shaky alliances are made strong...and the final battle for survival of a species is waged...
Make the main character a stand alone party in the war, aka fighting both sides. Let him slowly get more recruits until he has a full size army. They can go on sabotage missions and stuff, because their group is so small, they never get screened for it. Also, make him be partially cyberorganic, just for coolness factor.