The strange thing is that Petrach theorized about why Capella was destroyed, and perhaps that is the 'Official' end to the plot, resolving that shivans needed to use the small timespan between when they activated those large 'subspace guns' (after converging all their claw-like arms then letting rip with those giant black subspace ball things) , and use this energy to jump through some vortex that the quickly deteriorating capella sun could only provide enough power to do, perhaps to go somewhere. And if they've all gone away, then good riddence to them, since they've effectively gone somewhere and hopefully far away from GTVA space.