Tenebra is one of the antagonist organizations in the Stellar Incognita that Sagacious-6 will run into and even work with in many of the story branches. In fact, we know from the introduction that Sagacious-6 joined Tenebra after escaping from the mining colony where he was born.
Tenebra is a confederation of humans that oppose the power of the Sol Unity and Secura in the Stellar Incognita. Their goal is to establish a loosely-affiliated human society where every planet and colony is free to govern themselves as they wish, free from the edicts of GAIA and her representatives in the Stellar Incognita. But, according to GAIA, any humans outside of her control are unpredictable and destabilizing threats and must be brought into the fold.
Tenebra does not have a strong military or industrial base and it makes use of whatever its sympathizers can provide to it. Drug running, people smuggling and extortion are also common operations, especially where such activities weaken the Sol Unity's power and authority in the Stellar Incognita. There are also planets, colonies and systems that have joined Tenebra's cause and support them, but Tenebra cannot face Secura or the Sol Unity on even terms. However, what they lack in quantity, they make up for in quality. Their space interceptors are fast and deadly and their elite shock troopers are a serious threat to even the most highly trained enemies. But Tenebra must use their limited forces sparingly and apply them to where they will make the biggest impact.
At the time the story begins, Tenebra is being commanded by Spirou Georgiou and his helped by Kiyomi, the Chief Science Officer and Zizi, the Chief Intelligence Officer. They operate out of a large super-freighter converted into a mobile command center known as The Occam's Razor and this makes it hard for Secura to pin them down and eliminate the leadership.
The leadership of Tenebra is a hotbed of intrigue and double dealings and with so many competing philosophies, each area commander has their own local interests. Only the most wily operators make it to the top and thrive. The Tenebra leadership recognized early on that they can never hope to match the power of the Sol Unity and Secura, so they placed their bets on new and forbidden technologies, to tip the scales in their balance and earn freedom for the Tenebra aligned systems. It was in this environment that Sagacious-6 was recruited when he could demonstrate his achievements in cerebral research and nano-technology.