Steal from other campaigns. 
This is actually a good starting point. Other campaigns have their own storylines, but they leave a lot of room for "filler". For instance, during WiH's development, Darius made a mission focused on the Battle of Neptune, the very first skirmish between the Alliance and Tevs in the war, and The Blade Itself is set during Artemis Station in WiH's campaign. In addition, the ship description of the Erebus alone might give you some ideas of how the time gap between the Capella Supernova and AoA can be played out in missions, although I think it might be quite boring (simulations, drills, war games, Admirals Bei, Steele, Severanti and Armanjani having discussions and drinks among themselves, execution of the Threat Exigency Initiative, etc.).
Even the retail campaign leaves a lot of scope for the imagination. You could do a series of missions where you're a pilot stationed on the GTVA Colossus, follow the NTC Alexandria as it charged the Knossos with the Grall docked to it and explored the nebula beyond Gamma Draconis, or chronicle the history of the other Aeolus cruisers that don't feature prominently in retail missions.
If you find it daunting to write an entire campaign plot from scratch, try using the storyline of an existing mod and reimagine it in another mod. For instance, Inferno Release 1's plot in Blue Planet continuity would be quite interesting, I think, if it starts off with the Fedayeen nuking the other end of the Sol-Ross 128 subspace portal and creating an opening for the UEF to take the fight to Alliance systems like the EA did.
