In the first Secret Missions add-on to Wing Commander, the TCS Tiger's Claw responds to a distress call from the Terran colony in the Goddard System. Once they arrive, they find that the colony has been completely destroyed by a new Kilrathi secret weapon, with no survivors. The Tiger's Claw is then ordered to pursue the Kilrathi fleet into their own space and destroy this new weapon - without reinforcements or the ability to resupply...

The Secret Missions campaign adds 16 new missions to fly. Unlike the main game, there is no branching mission tree - progress is linear. There are also several new ships: a Confederation corvette, Kilrathi and Confederation freighters and of course the Kilrathi dreadnought with the secret weapon itself.

Characters from the main game can be transferred into the add-on, which also includes a "Mission Selector" to fly any of the missions from the original game.