maybe go with a couple of quests as Vee makes a lesser swarm under her direct command, and the big swarm comes crushing and destroys it, with a battle that is hard and challanging, but more quality then quantity, maybe introducing a new, even higher tier of enemy ship, made specifically to eliminate Vee and her rebellion. one where we need the ancient weapon we get from the vaultships.
maybe the end of that will also cause swarmships to target our pirate base in Illtari system, and be a reason why we need to build defenses there. with consequances of demolishing some of it otherwise - meaning that we need to repair the broken part of that base first.
And it could be an excuse to add content to the otherwise empty Xenos System - have Vee and us try to look into their secrets, in hope of finding somethin to help with the increased focus from the Swarm against us.
are Krell an all male race? havent seen any hint about female krell even existing...
I do agree that Stargate Atlantis and Star Trek would be good places to look for inspiration for more story line.
and if its not too much of a spoiler, was there a plan for whatever is behind the forcefield in the bot lab? it left me very curious and i hope something will be done with that.
as for additional content later, beyond the V1.60 - what about making it like the "Dragon age Origins: Awakening" expansion, and make it about appearance of a new foe and new zones. like those lizard people from Zabulon. maybe about their infiltrators learning that the MC is human, and not from that galaxy, and so wanting to capture him for study.