I am operating in the Star Trek universe as it was at the end of Star Trek Voyager (STV) - about 10 years later. I have added the destruction of Romulus, but not the alternate timeline of the JJ Abrams movies that include the destruction of Vulcan. I have no problem with the alternate timeline and I enjoy those movies, but that is not where I want to tell this story.
"Shipping" - I am not usually a fan of stories that are written only to explore romantic/sexual relationships. Kirk wants to screw Spock. Will Riker and Deanna Troi finally get it together. Seven of Nine proclaims undying love for Janeway - it isn't that these aren't stories that can be interesting, and there is plenty of "shipping" in my stories - but I prefer for that to be part of a larger story and only occasionally to drive the larger story. The big exception are "shipping" stories that are just explosively funny. I still find myself chuckling over some of those. So I try to explore the lighter side of lust and romance as well. Hopefully the climax of Episode 6 will mingle lust and horror in a way that you will find simultaneously funny and horrifying.
Hybrids - One of the central conflicts within this story is the explosive population of sentient hybrids. Spock was the first of these introduced - half vulcan/half human. I think it was Issac Asimov who observed you could more easily breed a man with a petunia than with an alien lifeform. This problem was addressed in Star Trek Enterprise (STE) - which introduced the idea that when a human and a vulcan want (or accidentally end up with) a hybrid child, that child cannot survive (and often can't get started) without extensive gene therapy.
Star Trek Next Generation (STNG) introduced the idea that all humanoid species were similar and could interbreed because they spring from DNA seeded into the galaxy by the Progenitors - the first humanoid species.
In the Star Trek original series (STO) the idea of a eugenics war was introduced along with Captain Kirk's greatest nemesis - the genetically modified Kahn Noonien Singh - memorably portrayed by Ricardo Montalbon and later reprised by Benedict Cumberbatch. As a result, the Federation has strict laws against genetic modification except to correct severe deformations - and (although this exception is never directly addressed) to make hybrids possible.
Star Trek Deep Space 9 (DS9) introduced the idea of people cheating on allowable genetic modifications while using one of the allowable exceptions. Dr. Julian Bashir finds out he was born with severe mental deficiencies, and his parents managed to cheat his genetic modification to illegally increase his intelligence and hand-eye coordination to super-human levels. A special exception is made in his case as gmods (illegally genetically enhanced people) are not allowed in Star Fleet.
DS9 also introduced Section31 - a secret accord written into the Federation Charter (which officially has 30 sections). Section 31 creates an extremely secret organization dedicated to protecting the Federation and preserving Federation democratic culture by any means necessary - even if that means fixing elections, assassination, extremely dirty tricks. Dr. Julian Bashir discovers this organization because he is intensely interested in spy stuff and grows suspicious about a few things - which were not loose ends left by the organization but were part of an effort to recruit him. Eventually he allows Luther Sloan - the Section 31 Director - to recruit him with the intent of exposing the organization. And finds himself in over his head.
STE introduced a man from the future who spoke wonderfully vaguely. When one of the characters ask if he was human, his response was "more or less". Captain Archer's crew did an autopsy on another man from the future (who died in the past) and found DNA from humans, vulcans and a dozen other species - suggesting the genetic future of humanity involved interbreeding with several different sentient species.
Star Trek Next Generation (STNG) introduced the Warp 5 speed limit. Centuries of warp travel has damaged spacetime. STO explained warping as a way of getting around the light speed limit and relativity problems of traveling in relative space. The ship does not travel through relative space, but instead warps space around it.
STNG also introduced the "Traveler" - a mysterious alien interested in propulsion. He becomes friends with Wesley Crusher and eventually takes Wesley off with him to explore very high end possibilities in space travel.
All of the Star Trek series were dedicated to showing a multi-ethnic, multi-cultural humanity operating in space as one species. The programs were breakthrough in providing leading roles for racial minorities and did not shy away from taking America's race problems head-on.
The reason for me to write these stories is the same as Roddenberry's - telling these stories is a way of telling stories about us. We can examine our problems from a different perspective.