Wing Commander: Secret Ops is set in the aftermath of the alien war that took place in Wing Commander: Prophecy. The super-carrier Midway's very best pilots are assigned to escort the Confederation's first "quick strike" assault cruiser: TCS Cerberus. The Terran Confederation Intelligence Service (TCIS) has slated Cerberus for 'deep cover' duty in foreign systems. Her specific capabilities remain TOP SECRET. But, to the Ace pilots from Midway, it is no secret that unrest is brewing in Sol and Vega sectors, that Kilrathi space (now littered with Alien debris) is a hotbed of looting and that the real WAR has just begun.