It's a bug linked to destroying the codex. If you take the other darkside option (give it to Darth Jadus) you can proceed fine.
I ended up doing that even though it isn't the ending I wanted, cause who knows when this is going to get fixed.
I have the same problem. at this point i'm in the same boat so I reset my quest to just take that ending but now my story is even more glitched. quest says "speak to fixer 12" and now fixer 12 is bugged and wont speak to me about the quest just how nice my ship looks... I just want to finish my story lol