Hey Gotcha,
after re-reading the lore again, I think I spotted a small mistake: the captain and crew that agreed to travel through the worm hole were banished because Hiigara might not be in the same "star system" as new Hiigara. Don't you mean galactic arm or, even better, galaxy instead? Given that the Hiigarans understood that they were headed to the uncharted Outer Rim, which is far, far away from their empire and Hiigara itself, I doubt that they would get particularly upset if the captain did his job. If, however the Hiigarans found that they are not even in the same galaxy, then things would be different. One of the key points in HW1 was that the Kushan found the Guide Stone within the ruins of an ancient city. After some analysis, they discovered that the guide stone was a star map/ image of constellations as seen from Hiigara.
Now, the thing about constellations is that due to its nature, prespective is everything. the big Dipper, for example, would look slightly different here on earth compared to say, another solar system deeper into the galactic core. As such, even if the Hiigarans were exiled, they knew that, in the future, they could always find and return to their homeworld, should the circumstanes permit it. However, if the Captain were to accidentally dump them into a completely different Galaxy, then this hope would be completely dashed, as they would not only need to find the specific point in space in the Galaxy, they would also need to find which galaxy it is, and then get there :O. Indeed, this explanation would actually be very canon friendly: it is generally accepted that the homeworld galaxy is not the milky way, while the star sector galaxy most certainly is. By saying that the Hiigarans were dumped into our galaxy, you can have your cake (New Hiigara is cut off from Old Hiigara and everyone else) and eat it too (everything is logical and lore friendly, yay!)
Also, regarding the captain's entry on 6535 GSY , 2840 Anno Domini.
I suspect that the captain would not be all too surprised to be honest. the Taiidan, Hiigarans and the Vaygr all look very Human like, despite all coming from completely different worlds. One of the theories that is floating around is that the reason for this is because the precursor race, known as the Progenitors, "seeded the galaxy with Life", and in the process decided to add human look-alikes to some of them. As such, in all likelyhood, the discovery of yet another human look-alike that had never been encountered, while somewhat novel, probably would not elicit a huge surprise from Hiigarans.
<.<
>.>
*puts on tinfoil hat* In the context of this mod, however, as well as how you set it up, you can have ALOT of fun with the above.
First of all, its important to note that it is stated in HW2 that the Progenitors were not native to the Homeworld Galaxy, which is pretty much confirmed to NOT be the milky way.
now, you can go the mundane route and simply say that the Milky way galaxy is simply another that the Precursors seeded life with...
OR:
significantly more terrifyingly interestingly, what if the reason why the Progenitors seeded the Homeworld Galaxy with human look-alikes was because they were the original human race? (or descendants thereof) What if, the wormhole not only sent the Hiigarans through space and into the milky way, but also through time as well, thousands of years back, as it were. when they finally re-discovered their home galaxy centuries later (Thus explaining their advanced tech), they constructed a huge ship (as Hiigarans tend to do), that eventually made its way into the homeworld Galaxy and, seeing it devoid of life, decided to seed life in Hiigara and elsewhere ect...
plot bonus: it would also explain why the progenitor chose that particular galaxy to seed with life as well as explains why the progenitor tech was stated to be compatible with Hiigaran tech in HW2 despite how unlikely two different computer systems seperated by thousands of years and differing species would have enough code similarity to be backward compatible. I mean, for crying out loud, we can't even manage that level of similarities between Apple Macs and Microsoft Windows! and that's between two companies, not two species with different biology, thoughts, cultures, taboos ect...