the Kobali part II has major game bug when you head to the hidden base for the first time because it causes you to skip all the way to the first choke point in Kobali part III
I did report it to Arc games and they said it's going to take time for them to correct the problem
so if you hadn't done Kobali Front mini arc, I would avoid doing it til they fix it
I suggest at least visit General Q'nel at minimum to advance the main Delta Quadrant story arc
you can still do the mission Dust to Dust without any issues
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On PC, I recently took a Gamma Recruit through the mission line without the described issue.