Zachary "Jazz" Colson, traitor to the Confederation, is being transported to his execution when he is freed by the Society of Mandarins. Meanwhile, Confed is testing its latest fighter, the Morningstar, on the Concordia. Performing the tests is the Wild Eagle Squadron, under the command of an old acquaintance: Todd "Maniac" Marshall. And while the Morningstar is still plagued with random failures of its jump drive, the Mandarin, under Jazz's command, have already set their eyes on acquiring the prototype for the Kilrathi.
The second Special Operations add-on to Wing Commander II adds a further 20 missions to fly. The new flyable fighter in the game is the Morningstar, which is armed with a tactical nuclear missile called the Mace, able to take out an entire fighter wing with one blast. Maniac returns as a wingman and brings the members of his squadron along. The story is told with the usual assortment of extensive cutscenes.
Player characters from either the original game or the first add-on can be transferred into Special Operations 2.