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Its a buggy quest and always has been. The only way I know of to get it to run OK for certain is to use the Unofficial Patch.
pc ps4 xboxone Brother Thomas unlocks the door to where Emogene is supposed to be but she doesn't appear. Instead the quest points back to Cabot House and the locked section of the house. Check the talk section of the page for a workaround for this bug. On PC this bug can be fixed using console commands, however on PS4 and Xbox One there is no confirmed fix. [verified]
This bug may occur regardless of whether or not one has kept the first serum. If executing 'fix' commands once one finds her missing, the serum will be removed (next quest stage) and one will be able to travel to Cabot House and talk to Jack. Commands: setstage 000503B9 70, setstage 00022A00 705, setstage 00022A00 710, setstage 00022A00 720, setstage 00022A00 750
Alternatively (and preferably), one can restore the conversation with Emogene by typing the following commands ssq ms09, prid 47ec4, ForceRefIntoAlias emogeneOld, ForceRefIntoAlias emogene, MoveTo 518ce, enable in the room where Thomas tries to "free you of your material life". Emogene will appear in the next room where Thomas is supposed to have locked her up in the first place. This way will make the quest proceed normally, without skipping anything.
above from wikia https://fallout.fandom.com/wiki/Emogene_Takes_a_Lover
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When Emogene Cabot isn't in that room next to the Charles View Amphitheater I just use these lines below in the console window to complete the quest and fast travel to the Cabot house and report that I found her
setstage 00022a00 705
setstage 00022a00 710
setstage 00022a00 720
setstage 00022a00 750
Mine is in a text document beside my games exe and I named the text em and just type in console window "bat em" to complete the bugged quest when it does bug up
Sounds like a rather complicated solution but looks safer than any others. All it's doing is putting her back where she's supposed to be with the console and restoring her conversation options.
Considering it's even listed as the preferred option, I would tend to lean on that one unless it doesn't work for you.
Yeah but it's a nasty, stupid bug. Ew, I forget all the arbitrary limitations survival mode has.
I use Survival Options to get back the console and quick save because of reasons just like this.
Although the best option would probably just let the UFO4P fix it for you.
And if it fails, I guess I'll just mod console commands in to fix the quest.
Yeah it was bugged before the DLCs.
And if the quest bugs out or my game gets corrupted? Eh, just a couple hours wasted. I'll go start a new survival game with mods enabled. Maybe try out Horizon again and get my ass handed to me.
What I do is for survival is I clear everything I need to in the Goodneighbor area in preparation for the quest. Then wake up first thing next morning and run it all the way through past meeting Emogene in the one day. The weird thing is I have never encountered the bug on survival doing this.
New game, here I come.