That's what I intend to do. The Stephinians are supposed to be very powerfull pepole who don't really do anything unless they are provoked. Then they completely obliterare the attacker. But they occasionally help independents (such as the player) and try to keep balance between some of the larger powers. So the player flies by Sectro (which comes a bit after heretic) and the Stephinians say hello and maybe upgrade his ship a bit for him (You'll need it!) and then he has the option of staying and doing things for the Stephinians (getting more recent technology, since the original upgrade will be quite outdated) and then proceeding twoards the core with some very powerfull friends, or proceed right to the galactic core which is faster, but much harder. The large Stephinian ships such as the HyperDestoyer (or Ego Vessel) and the Stephinian Capital Ship will only show up if you blow up a millitary base or start shooting at Stephinian ships. Balance may be a problem, but I'm expecting the game to be so tough enough at this point (I tink I'll only let you have the most powerfull weapons if you win to about 20-40 systems after Heretic) that most Stephinian weapons will appear just a bit off balance, but not much. Besides, if you go to the end of the current Transcencence, and then use a Gem Of Despair or a Transpace Jumpdrive to go back to Eradani, then they would seem unbalanced too.here's an idea- can you come up with a new line of technology that is interesting and balanced for the entire course of the game? Perhaps include some types of storyline and mission interaction for the other playerships to fringe benefit from, while making a core progression path for your particular ship.
And by the way, I made a few Commonweath Militia missions that involve the Ares or the Commonwealth finding little bits of Stephinian technology.