Ooft, I don't check in a couple of days and we get a bunch of new posts!
Basically, most of what has been said so far was my logical path. Even if I don't want to earn any money doing all of this, I still face the risk of being sued into oblivion by lawsuit-happy GW who have a track record of destroying small organisation.
I explored the option of acquiring a GW license. The requirements basically exclude myself currently - you need to be a studio with previous, published titles. Their standards may have slacked in recent years, but you still need to apply and be approved by their IP department. "Oh hey I want to make this retro-style game aimed for the hardcore stats-loving Chapter Master folks and no I don't have a team, or an experienced studio" is not going to get me very far. I am currently working on at least one title for another company that will reach Steam, but that isn't my studio, and it's likely not enough to get a license anyway.
The difficulty faced is that to garner the support of people interested in Chapter Master you need to make a game that looks, feels, smells and tastes like Chapter Master. How do you implement a generic, important gene-seed and founding chapter system? You just can't, without really stretching the genericness of your engine. I opted for DNA purity/mutation, but that also is really obviously geneseed and if it isn't it's just a racial purity game and has all of those problems.
If you do go full Chapter Master, you're just doomed from the get-go if you ever want to not get C&D'd, Or if you ever want to make any money from the project (and realtalk: you probably do with the huge time investment), you're almost guaranteeing a lawsuit.
So where does that leave you? You either abandon all precepts of Chapter Master at which point why are you even bothering or why would you not go pick up some other community that doesn't have IP issues (as Duke seems to have done with Tower Girls)? Or you make a genuinely different space game, in which case you're like any other indie game studio and have no following to begin with. It's really hard to find a valid way to make anything remotely Chapter Master if you care at all about your future.
And for the record, C&D demands can totally go beyond just "stop doing this" - they can demand repayment for lost income, basically anything, it's not a legal document so much as a list of demands and a rough legal basis to sue otherwise. So if they fire off a C&D and demand lost revenue, how does one deal with that? You either refuse and go to court and pay a ton of money, or you pay a ton of money, there are numerous cases online of fan projects being C&D'd into a corner by companeios that are making a point, and GW ahs a history of making points.
So, yeah, I'm still trying really hard to find a way to do this - I still am keeping in touch with the other people that worked briefly on SSME with me and am trying to come up with a good way to carry on the project as I super enjoyed the programming and engine building. It's just really hard to find a way to do it, nevermind find a way to do it that doesn't breach copyright and can generate some income so I can pay the artists, justify my own time vs freelancing to some extent, etc.
I welcome any ideas as to how to do it legally, safely and in an interesting way, but I'm drawing a blank right now.
TL;DR: Finding a good way to do this without being sued is really hard. You avoid legal battles by sacrificing specificity and stacking your product up alongside every other generic indie game except you're not an indie game studio and can't pay for art and sound and UI designers and so on, so you just lose.