So I was doing the quest as normal, having a rough time dealing with the onslaught of synths as my weapons are best for 1 on 1 type, so I ran into the tunnels under the armory, ran all the way through and came out of the east towers. now, there are no more synths, corsairs, or any enemies. only a quest stuck in 90%. it doesn't really matter what I do, I can not cause the quest to pick back up. is anyone else having this issue?

I feel I should reiterate and state this is the main quest defense after leaving the institute, they're attacking the castle to prevent us from "striking back"

Probably glitched out when you ran into the tunnels. Game was probably expecting you to stay and fight and thought you had gone onto another quest. At this point you have 1 of 3 option.

Option A) Ignore the quest and move on...(not really an option if you really want to complete the minutemen quests)

or

Option B: load from a previous save. (Times like this is why you really want lots and lots of save games)\

or

Option C: you could always try fast travelling out and back and see if that fixes it.