One thing I've always sort of thought of as a conclusion type storyline (which BWO if ever released was supposed to hint at it being the GTVA/Sol Reunion to prep for this) was to follow some of the early FS2 promo plot details.
Basically it's been a generation since reunification with Sol. The Shivans haven't been seen or heard from in over 30 years. The GTVA has insanely fortified the nodes that directly lead out of their core space and have sent relatively self-sufficient task forces for scouting the Knossos network. All of the ships have returned but one.
You're part of a recon in force sent down the path of this lost ship. The plotline basically starts as somewhat Apocalypse Now like with the commander of that taskforce going rogue basically arguing along lines of Bosch that the humans and Vasudans can't stand against the Shivans without some form of alliance. You're following more or less their path, seeing the ruins of species that the Ancients built themselves upon, etc. (basically this allows for fighting rogue same faction ships as in the first two games)
The climax of the first act being this CO using a high pulse ETAK signal and detonating a star (using what appears to be a constructed device by the commander based on Knossos technology). This shunts everything to the second act where new nodes have opened and Shivans begin an assault on GTVA space following the routes your fleet took. A major set piece being the destruction of the main fortified node that leads to the core systems and the Shivans sending through a Sathanas fleet that seems poised to detonate several GTVA systems.
As a last ditch effort and the third act, there is a new node discovered that leads to Shivan space. "Shivantown" being a type of dyson grid with dense subspace node formations that they tap for power. (basically the entire system is densely packed with nodes and sneezing wrong changes its configuration)
Using GTI and GTVI information, a modified ETAK to scramble Shivan comms is used and a weapon to detonate the sun (the GTVA's hail marry weapon based on the crazy commander's design) in the dyson grid is deployed (the same tech the rogue commander uses at the end of Act 1). It's a last ditch effort thrown at the weakest point of the Shivans with the hope of forcing them to at least cut them off from the bulk of their forces or make them withdraw.
As for the very ending, well the cycle of extinction and preservation ends with some real conclusions that don't involve a star child and red/green/blue explosions
Things like the dyson grid and some new Shivan supercaps would add in the "basically fighting on spaceship that's more like planetary surface" thing that was hinted at as wanted by Volition employees in a third game. The ships being done in a way that taking out subsystems (reactors for shield sheaths, etc.) by fighters and bombers is crucial for surviving although capships do the killing blow.