For now, storywise, they are just a device explaining how an isolated pocket of highly advanced space humans could happen, the rest is probably not yet finished at all...
...however, should we ever get to the point where the game's mechanics are finished (I see decades of fine-tuning in my crystal ball, though it's pirate-tech, so...) optional campaigns and missions with stories and characters behind them might pop up, as I hope, easily modable as well, so we can push our own treasure hunts and imminent doom device countdowns into the sector... and the gates could become a main story arc... what happened? Can they be reactivated or repurposed? Should they?
My idea would be to have a reason for the shutdown like Deus Ex, some radical but ingenious group that just got fed up with the universe-wide scheming of their rulers and shut it down in a way that made sure they would stay dead for a long time, creating localized pockets of space-faring humans - the corvus sector being a casualty as it was not yet self-sufficient... then get some research, space-hulk-hunting, corporate tech-stealing, the generic genius tech (maybe an artificial bio-tech brain in a 2-meter jar for a change?) to find a way to reactivate a gate at tremendous costs, and entirely seperate from that a research for what happened, followed by some major fight against the ruling powers of the sector that don't want the gate to be reopened, either because they fear being dismantled by more civilized domain authorities, or maybe because the shut down actually came with a more-or-less cryptic warning and explanation...
Then we could go full messed up stargate... connecting to random gates and find out what happened to that isolated part of the galaxy... happy agriworlds (to be exploited by the Hegemony...), reorganized sectors with their own powers and tech, rogue AIs having taken over, zombies, gate-malfunction letting in extra-dimensional terror-insects, etc. The options are endless, and could probably be fit into the game engine as it is, especially with some random generation now in place. I'd think that would be cool, because the endgame could grow with player strength and also reward unique and interesting spoils (capture an actual Domain Dreadnought preserved by some local warlord and used as a command ship/floating palace to rule over his subjects, just some nice worlds to colonize and exploit, the AI that just happens to be exactly strong enough to be a challenge to the player drops interesting new weapons... etc.)
Well. Don't we all have the fantasy-starsector in mind we want some time...? I'll shut up now.