Have you tried this ?
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If you get to the point where your in the Artus System (in the hanger) and your trying to talk to Watcher 2 in person and she keeps blowing you off, try this...
Get back on you ship then reset the A New Epoch of Fear mission. This should sent you back to see Darth blah blah. Go back and do that part of the quest again. Upon returning to your ship.. DO NOT click on your holo-terminal. Run right past it and travel back to the Artus System. Once there, DO NOT click on your holo-terminal. Go back to the Hanger and see Watcher 2 inperson, this time she should be willing to talk to you.
One the mission is finally over and your back on your ship, use your holo-terminal and you should get credit for completing "The Assassin's Fortress"
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I've been giving this advice out and it has helped several people.