Well, I had a vague plot based on this sort of scenario planned many moons ago.
The basic premise was that the SS Botany Bay was only one of the exodus ships, and that another group had also escaped Earth, under the sway of a rival of Khan who planned his escape from Khans core group and re-programmed the cryo pods to allow them to wake early. But seperated from the Botany Bay they were alone in the universe and on the brink of starvation when they were 'rescued' by another vessel...
And so they took over their rescuer and subjugated the survivors... But in so doing became hunted...
Cut to several hundred years later, when the heroes of your own saga come across a city ship, seemingly made up of a rag-tag fleet welded and fixed together... although scans show that its not quite as patch-work as it first appears with reasonable up-to-date weapons, shields and engines comparable with most contempary powers... And the crew is a motly collection of species led by advanced humans, decended from the original crew...
Now you can either go with a slave-owning race of arrogant super-beings, still modifying themselves, and acting as space-pirates, generally disreputable, and about to become a protagonist and general pain in the lives of our heroes...
Alternatively, over the centuries they may simply be on the run from the various civilisations that their ancestors antagonised, genetically programmed to fight, they need help and could well use the guidance and may even seek repatriation over the course of a series (if any of your players ever fancy playing a genetically advanced human???)
DanG/Darth Gurden
The Voice of Reason and Sith Lord
“Putting the FUNK! back into Dysfunctional!”
Coming soon. The USS Ganymede NCC-80107
"Ad astrae per scientia" (To the stars through knowledge)