Secret Ops continues the story of Wing Commander: Prophecy.
Casey and some of his wingmates are transferred to the Confederation's newest cruiser, the TCS Cerberus. They are assigned patrol duties close to the Sol system.
However, the bugs are back and this time, they are close to Earth. It's up to Casey to stop their plans once more.
Secret Ops uses essentially the same engine as Prophecy. You can fly upgraded versions of the Prophecy fighters equipped with some new weapons. The story is no longer told with videos but with cutscenes using the game engine.