In the second add-on to Wing Commander, everything seems quiet at first. The Tiger's Claw is stationed in the Firekka system. The Firekkans are bird-like aliens who are applying for membership in the Confederation, with the Tiger's Claw watching over the diplomatic negotiations. Things change when huge Kilrathi fleets appear near Firekka. Even though the system has no military value, the Kilrathi are pulling fleets from other systems, all of them heading for Firekka. The Confederation is puzzled, until a Kilrathi defector is able to shed light on the mystery and the pilots of the Claw are called to defend Firekka and the Confederation diplomats from a Kilrathi holy war.
The add-on adds 16 new missions to fly, with a linear mission structure. New Kilrathi ships include the Hhriss heavy fighter, the Snakeir strike carrier and an upgraded version of the Dralthi. The player gets to fly these new Dralthi, provided by the Kilrathi defector, in special undercover missions. Many of the Kilrathi fighters are now manned by the Drakhai, the elite Imperial Guard, while the Confederation's defenses are reinforced by two new wingmen, Doomsday and Jazz.
Player characters from both the original game and the first add-on can be transferred, and the Mission Selector from that add-on, allowing one to play any mission from Wing Commander, is also included.
Secret Missions 2 actually has a new executable: SM2.EXE instead of Wing Commander's WC.EXE. This new EXE incorporates multiple changes and fixed a couple bugs.
With a bit of file copying, it is possible to run the original WC and SM1 missions with the new EXE. However, the Dralthi will be the Mk II version (with mass drivers, more lethal) and all references to Bossman and Paladin will have Doomsday and Jazz displayed instead.