From what ive been reading so far alot of people have been having the same problem i ran into while doing these missions. After you complete looming shadows the quest line mysteriously ends. I tried the fixes i found from googling and well they were way wrong and a waste of alot of time. I havent found any fixes listed anywhere. So while i was sitting here staring evilly at the act 2 listed under episodes wishing it would work right i noticed that mission between act 1 and 2 called capture the flag. Looks totally unrelated and not list anywhere as part of the mission arc. Well apparently it is!!!!!! Click skip and hopefully act 2 will become available for you as well. Hope this helps. STO you can mail me a fat check for doin your job for you.
Open missions log
Click the delta quadrant
Find and skip capture the flag or try playing it up to you
Act 2 should be available