Season 3, Borg Missions, The new Enterprise, and absence of Enterprise-E from the game thus far. It can be pieced together in one season.
I know the season three missions are likely to be planned but I would like to summerise how I'd feel you should go about with it.
First off, Brent Spiner. Bring him in for as a Voice Actor for Captain Data.
Secondly, Enterprise must be a centerpiece to finally end it's long run. The ship is roughly 30 years old and hasn't been heard from as much since the Hobus Event.
So here we are. Borg, final chapter or a step back for the collective. Put them away from an expansion or two.
Episode One: Rendevous with the Enterprise, carry out a recon mission over a direct Borg threat. Episode Two: Engage Borg ships in such in such, some instances with the Enterprise. Episode Three: No Enterprise, investigation into the borg's tactics. No combat, more infiltrating ... A cube maybe? Find that the borg are creating an assimilation Virus that could spread across 3 sectors. Episode Four: Distress Call, Enterprise, Eliminate the Borg Sphere, and board the Enterprise, move the information from the Databases on the Bridge and help evacuate many survivors to Escape Pods (Transport is impossible after coming aboard). Get to work on the Radiation prevent Transport and beam back, evade and escape the Tactical Cube, leave system, Cutscene? Episode Five: Return to the System, disable the Tactical Cube's Warp Drive, They redirect power from Warp power to shields. Their shields regenerate faster than your weapons. Board the Enterprise, use it's Warpcore to destroy the cube via collision.
Earn an Android Bridge Officer.
Paves the way to a new Enterprise.
Yeah it's a bit one faction sided but it be adapted for Klingon equivilant.
With Series 3 scheduled for early Jan and the Enterprise contest not starting until early December I think it's a safe bet that Series 3 won't be about the Enterprise. It's certainly a possibility for Series 4 or 5, though.
As for Spiner, I won't say we'll never see him in the game but it was Dstahl who joked that Cryptic was going to need to put a $150,000 c-store item up for sale called Brent Spiner so that they could afford to get him.