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.
All the "cut-scenes" in the game are rendered in the game engine itself. While this is nothing really new (Starsiege did that long before Secret Ops), it was a first for an Origin game.
Secret Ops was distributed for free over internet, being one of the earliest games that was split into several downloads that were released at different times. Starting August 27th, 1998, when the basic game files and the first missions were released, a new episode containing six to eight missions was made available weekly over a period of seven weeks. These missions, were activated with a code you received when you finished the last mission of the previous download. Fiction leading in to a new episode was released on the Secret Ops website a few days prior to the actual episode release. The scheduled releases ended on October 31st, 1998.