The end conversation with Obisek I didn't understand. I did the diplomatic choices and he allowed me to explore the Vault but not leave. I expected my science officer to inform me of a plan to get out and away but, no, I had to reopen the dialogue tree and provoke him :S I'm not going to nitpick though
Job well done Cryptic. Nice set up
HMMM ... actually there was one option (can' remember the exact wording now ) .. but his final response was some what apologetic ... but then end was still the same .. time for you to leave .. in a diplomatic bag (so to speak).
In short you were still going to fight your way out.