If the galaxy has had other large events in the past that line up with the other galactic extinctions then you might be onto something.
I don't see how that could cause it, the speed of light would prevent any direct effects. But perhaps the two events are related somehow.
With some more research, It seems that it WAS A NATURAL PHENOMENA. Just much, Much, MUCH, M U C H, bigger than a supernova, Turns out it seems that you parished at about the same time meshorsha's SMBH exploded with an anti-matter white hole, We are unsure as to why your ships got devistated, but other ships didnt care, But we think its because your ships didnt have as much as a magnetic field.
Actually, if you have any tracer ships, I suggest you use them to gather as much information as you can, this event has occurred before, it seems likely it will happen again.
An EMP wouldn't have been able to cause it, nor any natural phenomenon. If you took some precise measurements to find when exactly each event occurred you might be able to find the source of a signal, although anyone advanced enoungh to do this would hide the signal.
Was there any suddenly bright lights just as soon as it started happening?
Possibly an EMP blast at a mega scale, Could be caused by massive supernovas...
If you want some details about what happened, Every ship except for ones inside the event horizon of the supermassive black hole and 23 prototype ships suddenly lost contact and either self destructed or fired on ships that were unable to self destruct. The only black holes formed that we know of were in zones 1 and 3.
The Dreii empire was destroyed by their own ships. We don't know who or what caused it, but the technology required to do so is way beyond what we thought was possible for anyone in the galaxy.
The antimatter transport ship arrives, And gets in a 100000 Kilometer orbit around the planet. Ready to transfer antimatter wherever its needed, And it still has plenty of FTL fuel left in it. It also comes with a message asking "Who destroyed the dreii, We will punish them for there wrong-doing, If it wasnt a seperate faction, We will do our best to see what weant wrong. As many details as possible is preferable."