I've been to a lot of places in the mod, whacking boss after boss (I find them a little squishy for my tastes, probably because my fleet is EMP heavy? Not entirely sure but they seem to go down mega fast with me) and this has me going through the storyline probably in a really weird sequence. My first place to go was the nullspace one (I managed to get in after getting the updated version of Fleet Journal!) and nailed that so early I didn't even have gates. I had to transverse my way out, then eventually picked up the other boss at the cache in the Alpha Site after dealing with ziggy.
After that, I nailed a few more - I got Amaterasu in the Elysian system as I went wandering through there again, and then went I and did Dark Deeds with the Tritach story. It sent me to the Luna Sea system, a great big blue giant...but there's a catch - it says that the ship is orbiting a jump point in that system, but there's just the one point (called Second Trial), and there's no ship near it. Is it somewhere else in the system? I'm not so sure where to go next there.
Also, is there anything to do with the white hole in the null space area? I found the derelict fleet and killed the boss in there, but that seems to be it according to the neutrino detector, I think. I'm terrible at finding stuff with so many nebulae around
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