In the end, humanity could only save four systems.
The Exterminators came without warning, with ships more powerful than anything the humans could construct. Without even an attempt at communication they set about destroying the far flung interstellar polities they encountered.
It didn’t go all their own way of course, humanity always developed rapidly during times of crises and this was no exception, by the time the end came all the factions had united and shared what they discovered, that the Exterminators only goal was the destruction of interstellar civilization. Suddenly the ancient ruins discovered in dead systems, and the lack of other interstellar empires was explained. Although the why of it remained a mystery even until the end.
If given even a few more decades, perhaps things could have gone differently, but unity took too long, and too much was lost, humanity lost the numbers needed to defend itself even as its technology reached a level where it could compete. Plans had to be made for the survival of the species.
Jump Point theory was expanded, and attempts to slip “sideways” out of reality were made, slower than light colony ships were launched, with millions in cryo sleep on long eccentric orbits of their homes, or sent to distant stars with no known connection to the jump network. Exploratory fleets fled deep into space, using jump points as soon as they were discovered in their attempt to escape the reach of the Exterminators.
To the best knowledge available all failed. In the end, the Exterminators found and destroyed them all. In the end fleet remnants in four isolated systems near the periphery of known space came to the same conclusion: If the Exterminators targeted civilizations, then perhaps they would leave if there were no civilizations left to target. They bombarded their own cities, factories, and space stations, destroying, disabling, or taking apart anything that would generate a TN technological signature, and then hid themselves in the coronas of stars, or deep in the gas giants of their homes.
In these four systems humans survived, through heart breaking effort they relearned low tech ways of survival and rebuilt. Saving knowledge in unique ways and developing on their own, for centuries.
Eventually hidden sensor networks in old Human space detected signs that the four worlds were reaching space once more, and that once again they would attract the attention of the Exterminators, the only question was when. Signals were sent, and the mothballed fleets awoke once more returning to the worlds they devastated but this time as saviors, the knowledge in the fleet databases was quickly absorbed and humans began their return to the stars, using a combination of ancient high technology and brand new primitive Trans Newtonian techniques. They now knew what was coming, although they did not know when or from where
In the meantime there were dead systems to loot, new ones to explore, and other humans to squabble with as well as other dangers both old and new.
