I accidentally triggered something in Covenant and they all began attacking me and I had no choice but to kill everyone in town and all the sentrybots.

I got Jacob's password but it doesn't work when I go to the terminal that requires it.

Even though it's in my inventory it doesn't work.

Any suggestions?

Reload.

there are actually two areas that require Jacob's password :/

one in Covenant and one in a facility not far from it

and there seem to be also two different Jacobs and two passwords?

maybe you have the wrong one?

There are two different Jacob's Passwords in the game. One is for Covenant, one is for MacCready's companion quest which takes you to the Med-Tek Research Facility. You can get bugged regardless of the order in which these things are completed. Giving these items the same name was a bad move.

See if you have two 'Jacob's Passwords' in your inventory. If so, try removing one from your inventory, and then try the terminal again. If it doesn't work, try it with the other one.

Nope I've only got one so far. So apparently the one I have ( which I found in Covenant ) is not for Covenant but for the other place, wherever that is.

I suppose I will eventually find it.

Have you done MacCready's companion quest yet? That's where it would be from, if it's not the one from Covenant.