Curiously enough, I had a very vaguely similar idea a while ago -- inspired by a different source, though.
There's a very old Marathon addon, "Return to Marathon". The idea of the story is that you're coming back to Earth on this new ship; you've been in stasis a long time. Along the way, your ship drops by the original Marathon, over a hundred years after your original campaign there, and the computers onboard your ship detect activity. Thus, you're woken up to take a look.
Most of your old weapons are long wasted away. Your pistols still work perfectly, and you still have your fusion gun (though the batteries are very weak, after so much time), but most of your other stuff is broken, lacks ammo or requires alterations. Your napalm unit is converted into a makeshift jetpack.
You leave your ship through an airlock and go over to the Marathon. Everything's gray, and there's this "thumping" (the sound of your air systems). It looks dead creepy.
When you get to the Marathon and find an entry point, the ominous factor turns up even more. You walk through old corridors, rusted over. Weird, incomprehensible and rather scary living "blobs" hang from the ceilings; they don't respond as you destroy them. The corridors are oddly quiet.
You go through places you saw, chronologically, a hundred years before. You find the first terminal in the original game, where Leela made her red alert. You can't access it anymore. The entry door you started at has some random stuff behind it. The layout's the same, but things have definitively changed.
The effect was scary, and I was inspired by that idea -- looking back at something long after -- for an EV plugin.
A "return to the EV universe".
There'd be some missions on the Nova side, possibly Kontik probe, and you'd find a way to access some new systems...and then you'd step into the past.
You'd enter through and find these old systems, named identically to EV. But they'd be uninhabited, or some such. Ideally lots of ruins. It would become obvious after a short time that something very wrong went on there.
I think I had the idea that the aliens came back and killed almost everyone; if not that, then presumably some terrible intra-human war. At any rate, there'd ideally be a few alien ships, and a lot of automated "battleships", made long ago. Sometimes still fighting it out, almost all willing to attack you, as a foreign intruder into their space.
You'd meet enemies around every corner, and the galaxy would be in such a horrible state of disrepair. You'd be able to pick up some ancient ships there, like Corvettes and Kestrels and Confed Cruisers, though their effectiveness would probably be blunted with time. Possibly also more recent ships, made during the wars after EV.
There'd still be a handful of humans, but they'd be xenophobic and resistant to your arrival. Their automated defenses would attempt to destroy you at all costs anyway, so it's not likely you could land on the planet to start with.
Your idea here sounds really familiar to that -- and so I think it's a good idea. If done right, it'd be very atmospheric. Spooky, maybe a bit sad.
If you're inclined to try it at some point, go for it.