I've already started on a campaign - a crossover of sorts, with the Shivans invading federation space, forcing starfleet and the GTVA to ally against them.
The first mission was that crappy one i made, with the demons and the enterprise ambushing it. It was more for show than anything else (but it IS complete in a sense), but my second mission (which is complete, and i will post in a few minutes) continues the plotline a bit further, with the appearance of Admiral Bosch in federation space

The 3rd mission will be back in GTVA space, where Admiral picard makes a bold move to make contact with the shivans, and prevent them from sending capella into nova, but the ending is a twist that im not going to reveal just yet. The 4th mission is back again in Federation space, this time at the hands of a massive Dominion incursion into DS9. But, the dominion are not hostile, as Shivans start to pour out the wormhole , chasing them down. After a tough battle, most dominion ships get to safety, and the wormhole is secured to prevent the Shivans from coming in.
Mission 5 is again back in GTVA space. This time, things have taken a turn for the worse.
I intend to create a >12 mission campaign with these ships - the plot potentials are vast, including twists, turns and unpredictable events mid-campaign (the ideas of what i can do with Bosch alone are pretty numerous)........
But thats a crossover thing. If you want pure ST campaign, then consider this one:
The basic scenario is that Alpha wing is the only fighter wing alonside a large group of pirates. These pirates have captured mostly old vessels, like the Constitutions, Excelsiors, and a single Akira from the past raids. The Federation, the victim of such succesfull strikes, have finally given in and called the Klingons in to help eliminate them. The potential for plots here are also huge, but i'd rather not give anything away at this conjecture.
If you want more, just ask.