I went to Fort Apogee to join the Protectorate, after Ambassador Athanas' suggestion. I entered Fort Apogee, then tried to enter the second area of Fort Apogee (the one with the medic) before talking to Consol Oliver. The guard stopped me with dialogue about not being allowed to enter this area currently- I said "OK, I am going to Oliver" or sth like that. When dialogue finished, I was in combat mode and everyone was hostile.
(Might have something to do with having clicked beyond the guard before his dialogue stopped me? Not sure, but I didn't enter the restricted area.)