No, I also had this happened to me.
I got a tip from another player, saying I should go down the beach (behind the nest towers) and kill the Black Ring there. Then, go to the teleporter on the left of the 2 nest towers, a bit above, and then use the teleport there to get into the Bunker. Take out Lord John and Lady Kara there, go upstairs, either choose to kill the 2 Black Ring up there or choose to spare them and be able to buy items from them (I chose this one). Then, flick the 3 levers in the room of those 2 Black Ring, and most of the sheilds in the Orabas Fjords will be taken down, and then you will be able to access most of the areas and quests.