Released free via the Internet, Wing Commander: Secret Ops was structured differently than the previous Wing Commander games. Instead of a standalone games, Secret Ops missions were released episodically via the Internet for free download.

This time around, the evil Nephilum have used a second jump gate to attack your home more directly, and they also have a deadly new viral weapon. You, along with a small band of TCS Midway veterans are assigned to counter-attack in a quick and effective strike against this new threat.