When ideological wars on Earth started getting bad, and technology was such that people worried about an extinction level event, old plans to have a substantial portion of the population leave were enacted. The colony ship Warden was constructed and sent out, only to return with the Canopus Plague, a hive mind created by another alien race to infect intelligent creatures with an impulse to kill each other (the goal being to leave habitable planets to settle if/when they arrive).
The plague was soon quelled in its active form, but carriers were by then already setting up a new organization which would eventually be called Armageddon. They started threatening the world with end-times (and amassing the technology to do it) if the world didn’t cease warring. This supposedly noble cause was a front, however, and they had no intention of not using their weapons, counting on this front to give them room to wiggle and negotiate until they were ready to strike. A more militant, less organized set of the infected called The Friends of Entropy tended to be much more forthright in their destructiveness, but were curtailed by the wary, therefore.
Another colony ship, the Legacy, was put together rapidly with some serious design flaws (impossible not to have these in a thing this complex created in so short a time). The ship left, but not before folks who were members of Armageddon and The Friends of Entropy managed to get aboard. Not long after the Legacy’s departure, sane forces on Earth discovered the true nature of Armageddon and what they were about to unleash, which were radiation weapons designed to mangle DNA and destroy all life on Earth.
In an attempt to mitigate the disaster, researchers created nano-bots that they hoped would be prophylactic against this weapon, which necessitated having think-tank organizers that had the DNA codes on hand. As a safety precaution, these plans were sent to the Legacy so that if things went wrong, perhaps the Legacy’s people could return to Earth some day and set things right. Meanwhile as the message went out, the weapon was released. It would have been thwarted by the nanites, except that the think tanks controlling them were also affected by the weapon. Their information damaged or erased, the nanites re-arranged whatever DNA they could find into whatever viable lifeforms they could manage out of the few living specimens left. The result are the new denizens of the Gamma World.
The message arrived at the Legacy years later, only to find the ship itself in a state of war arranged by the Friends of Entropy elements that were onboard. The conflicts they had set up were largely about whether or not it was right for the people on board to have been sent out from home, the later generations without having been given a choice (lifespans on board the Legacy were not quite what they’d been on Earth, and it the ship had been on its way for centuries). The FoE elements were working on developing the same weapon to use against the people of the Legacy, but did not have the radiation element necessary. The forces of order managed to recreate the nanites that Earth had just as the FoE managed to figure out how to use their weapon by swinging the Legacy through a radiation cloud perfect for causing the weapon to function as needed. Therefore the events on the Legacy played out similarly to how they had on the Earth, with a tiny population surviving due to the efforts of the damaged think tank driven nanite swarms.
The crew, seeing this happening around them, put themselves into suspended animation with orders to only be woken by Ra, the central think tank, once things had settled down to the point that they could help. Ra, however, understanding that it was about to be affected by the gamma weapon, put itself into stasis as well, putting a key out in the wilderness where the FoE elements attacking Ra would not be able to find it, waiting for a day when one of the other think tanks would be sane enough to figure the situation out and fix everything.
Dowin is on the verge of figuring things out after a few long centuries insane rebuilding and repair, and is now looking for the key to Ra, to set things right again… or at least Dowin’s vision of right.
The nav systems having been set on automatic long ago, the Legacy has now in its travels visited not only its primary destination, but, no crew having told it to stay put at that site, has moved on to a second system.
What to do with the Legacy? Where to colonize, if anywhere? Go back to Earth? Blow it all to hell?