Recently I'm being reaquainted with the Macross with the new anime Macross Frontier.
In the middle of Macross, Earth got orbitally blasted by 5 million ships leaving only a million survivors.
What remained of the UN government with their new Zentradi allies, who integrated to human society, formulated a plan so that the human race would never have to face extinction again.
The colonization plan.
Utilizing city ships with armed military escorts humanity would spread around the galaxy ensuring that all their eggs are not in one basket.
Now seeing that basically the Ancients faced annahilation three times that we know of.
Wouldn't it be smart of them to spread around the galaxies so they wont be extinguished in one galaxy?
We know there was at least one other city ship in the Pegasus besides Atlantis.