I'm not sure how Bethesda missed this one... The Armillary connects to your grav drive in order to jump to the Unity. However, if you do not want to start a new game, you must remove the Armillary from your ship. This all makes sense. What doesn't make sense is that building the Armillary at an outpost somehow still triggers you to grav jump to the Unity, so the only option you have is carrying around the stupid thing in your inventory. Would love to see a mod that can fix this.