I was fine when I ran into the bugs where I couldnt defend my settlements and I lost a few people and had to repair a building or two.

Now I have run into a game breaker for me.

While doing Emogene Takes a Lover, I finally track her down, only she isnt in the room. Its empty. It sends me back to Cabot House to find her behind doors that require keys that I dont have.

I used a series of console commands I found on some forums:

setstage 000503B9 70
setstage 00022A00 705
setstage 00022A00 710
setstage 00022A00 720
setstage 00022A00 750

Speak to Jack about Arabia, then try to get more information from him.

setstage 00022A00 800

Once you enter all those the quest will be marked complete and a radio in the house will go off and Jack will respond to it progressing the quest line.

Minor Spoilers, I am keeping it vague so no one knows too much about this unless they have already learned about these people.

That actually worked, except when I started on The Secret of Cabot House, I get through the asylum and Edward Deegan is not by the elevator. So Jack Cabot is kneeling next to no one to start the dialogue sequence I saw in a youtube Let's Play video. Again, no big deal, I figure I will just go about my business and wait for a patch. APPARENTLY you can fail the quest and fail to prevent the raiders from freeing Lorenzo, but it still wont change my objective or update the quest. I have reloaded my game all the way back to Emogene not being in the room and supposedly being in Cabot House. (I did clip through the wall and she is not where the quest indicator says.)

I have the exact same problem. Emogene actually IS at the marker, but is invisible. You can make her visible by using the console to kill and then resurrect her, and when you try to talk to her, your character will even speak as if it is related to the quest, but she does not answer. Disabling and then enabling her AI doesn't work either. I spent a good three hours messing with the console in an attempt to fix it in a way that ultimately allows me to complete the quest chain, to no avail. I even went back to my save just before leaving the vault, left the vault, immediately turned clipping off and flew into the room she is supposed to be in, and still she was invisible.

At least in my case, whatever it is that causes her to be invisible apparently is initiated very early on in the game, probably when NPCs are first created in the world, since I could not possibly have done anything that would affect her before even leaving the vault or on the trip there. Next step is to start a completely new game and fly out again to see if she is still invisible. Even if she is not and the quest works, I will be kind of paranoid to continue because what if I get 30+ hours in again only to find some other NPC suffering the same fate!

Oddly enough, despite their buggy reputation, this is the first Bethesda game that I can recall having a serious, quest-breaking bug actually happen to me.

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