I, too, have run into this issue. You can get to the Vigil, Priory, or Secrets headquarters via the Asura Gates at Fort Trinity, once you’ve advanced far enough in the story line; but once at an HQ, you are not allowed back to that particular Order’s Asura Gate to return to Fort Trinity. Interaction with the gate blocking access to the Asura Gate refers you to talk to the Gate Guard. The Gate Guard NPCs simply say that this area is under construction.