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To be edited

years 0 to 1. refugees settle our planet, "Dross" (derived from "Drawstraws", an unfortunate period in the planet's settlement when there were more people than room and supplies for them)
years 0 to ~600. Societies of Dross grow underground, unnoticed by the outside world. Some cultures isolate themselves in their caverns.
year 635. A corporation discovers the presence of exploitable biological resources on Dross.
year 636. the Corporate AI/board of directors deems an expedition to Dross to be inefficient at this time. Howard-David's boss disobeys the AI and sends a mission, which he is sure will be profitable and worth the risk. Even if it draws down the ire of the slavaers on the Corporation, he intends to jump ship with his profits.
year 637. An expedition is sent in secret to gather biological resources from Dross, including a specimen, technically unknown but whose existance has been extrapolated from ecosystem data, which supposedly will be worth much. Most of the crew and scientists don't know their mission is unauthorized, only Howard (as financial overseer) and a few ranking officers know the truth-or most of it, anyway. It is not the bulk resources that are so much valuable, but rather the information, the genetic codes contained in the lifeforms and the overall structure of the ecosystem. As well as individual specimens genetic makeup being valuable for medical and warfare reasons, the sum of a unique ecosystem can be used to gain insight in advanced mathematical models, essentially, if sufficient information is gathered, having the potential to make the AI smarter, more powerful. Howard's boss intends to gain wealth and power from his AI sponsor with the success of this secret mission. Howard himself intends to steal or copy the results of the mission and sell it to a rival corporation. Who knows what the the other expedition members want to do--mostly just get paid their wages and a small share of profits for their work, but some recognize the suspicious circumstances and may have their own plans. And of course the ecosystem itself, as well as the inhabitants of the world, will throw this small expedition a few surprises.

That is my summary. Clearly several elements conflict with your path. Which ones do you want to resolve?
here is a copy of my master timeline.
4307 AD is when colonization beyond our solar system begins. In the next century or so would be when the First Step Colony world is colonized.
4520 AD this would be about 0 on your Dross timeline.
5150 AD Empire of Mars is conquered by slavaerlords (Slavaers start on Earth) as are all settlements in the solar system. This is when colony worlds begin serious thought of last stand/evacuate scenarios. So this would be around 630 on your Dross timeline.
Okay so doing a little blending.
~158,000,000 BC Dross was initally a secret base of the vnugans, almost a 160 million years ago. They lived and experimented deep underground. They created subterranean ecosystems as part of their habitats--to be comfortable. Over a period of 10,000 years they crashed a half dozen comets into the planet as per their typical terraforming efforts. These comets added a substantial amount of life elements to the planet's surface. The caindas found and wiped out all life on Dross (still ~158,000,000 BC).
The "slug" race I mentioned before were very carefully made to resist evolution. The vnugans were afraid of the very real possibility of creating a slave race that evolved into something that could challenge them. So after a 160 million years they are not much changed. The caindas didn't wipe out the "slugs" but did make sure they avoided planets--and so became purely spacefaring. Trading with outside races (humans) is a new thing for them (or a long forgotten thing).
4520 AD The One and Twelve sponsor a secret colony to be founded in the caverns left over from the vnugan base. This is one of a number attempts. The One and Twelve want to live their way in peace and since they want to spend most of their/all of their time plugged into the second universe living underground is not a constraint or psychological problem.
Something goes wrong, two of their three supply ships or storage material never arrive. Even with redundancy and rationing they have 30-40% more people then they can support. In addition some vital equipment is unavailable.
5100 AD Jump forward 600 years. The survivors of Dross may have unlocked some of the fossilized secrets of the vnugans to help them survive. Some managed to create a second universe network which allows their bodies to kind of hibernate and thus use up very little resources.
Howard-David on the First Step Colony World looks to Dross which was just purchased by his corporation for some reason. He is fascinated with something. Maybe he learned from the "slugs" that this used to be a planet of their creators. His company's AI may know that Dross was secretly colonized by the One and Twelve just before they were banished from Earth.
So two possible interests/reasons. Maybe the AI bought it because of the active second universe it sensed there, and Howard-David got interested because of its ancient alien history.
The "slug" sub race is a new creation I made for this story so I haven't entered anything about them into my master files yet.
Note that the organic mining machines come with Howard, so as of 630 Dross time the cavern system is relatively small. It is only after a few centuries that they cavern system becomes truly epic.
800-900 Dross time.
What do you think? Is this working, can you further splice this?
Instant messaging would work. I have Yahoo, you know that. that would be easiest for me, since I often use it to listen to music, and have it active for emails and what not.
Let's have the main narrative start at year Dross year 0. We could do it in segments. A series of short stories, sort of like the Man-kzinn wars if you are family with that sci-fi series.
First story at year 0, last story at year 3000 or something, at which time they connect with offworlders and get civilized--take to the stars etc.
between 0-600 they have very limited connection with outside world. First off because their mission was secret and the One and Twelve group is oppressed. Second they lost much equipment and maybe a good portion of their ability to communicate off world easily.
When they get their second universe up and running they could have some contact through the Ayrt universe but it would be slight/fleeting and their location would still be a secret.
With Howard they would initially have contact with other worlds but as the slavaers expanded towards them they would cut off contact, probably just to some light trading.