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You don't need to kill him, you can talk him into letting her go.
Copied from the info link
"It's a short walk to the Charles View Amphitheater where Thomas is holed up, speaking with him results in a few options being presented: bribery, persuasion, or threatening Thomas. Alternatively, the locked door in his office can be picked to set her free. "
Unofficial Fallout 4 Patch
https://www.nexusmods.com/fallout4/mods/4598
And further down that same page :
https://fallout.fandom.com/wiki/Emogene_Takes_a_Lover#Bugs
PS: I'm onto my 4th or 5th playthrough of FO4, with the Unofficial Patch, and Emogen appeared in that room only once.
You can move Emogene next to you and make her spawn by opening console and typing these lines to it:
prid 47ec4 (makes the console target her)
moveto player (moves her next to your character)
enable (makes her spawn)
Then you can talk to her and continue the quest normally.
This is how it worked for me:
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.
Source: https://fallout.fandom.com/wiki/Emogene_Takes_a_Lover
check fallout fandom with the name of quest and see which stage you are in and take it to the next one.
command was "setstage [questid][stage]" if i recall correctly.
As stated in the Fandom, the commands to fix exactly the issue of her not spawning is:
ssq ms09, prid 47ec4, ForceRefIntoAlias emogeneOld, ForceRefIntoAlias emogene, MoveTo 518ce, enable.
Ah yes, it's stated in fandom page bugs section. Thanks for the update, next time i'll use this if i encounter the same ever again.
Patch can not do retroactive fixes to script data that is already baked in to save files.
So, yeah. Patch needs to be enabled prior of reaching relevant point in the quest line and preferably before starting the quest line.
I actually do not recommend this at all. While it sounds like the "correct fix" I seriously doubt it is. I think the only real fix is the UOF4P mod applied prior to the quest.
The actual issue with those last two Cabot House quests with both Emogene and Jack is the scripts get confused because the old and younger versions get mixed up. Both NPC have age versions with separate ID#s. Jack is just less frequent.
Now the problem is by changing the alias you are not ending the scripts for the other versions properly. Which means their scripts remain broken or keep running.
If everything runs correctly you can encounter Jack as a random encounter:
https://steamcommunity.com/sharedfiles/filedetails/?id=1291903339
Emogene can be found in the Third Rail which can be either the younger or older versions.
The other thing is if you do not process the second quest properly it will screw your third quest. The fix on the wiki is unlikely verified to prevent that. The setstage commands listed in the other two topics are a known fix that does not screw the third quest.
I tested both commands to teleport old and young Emogene to me, but none worked because she was never spawned at the world.
I follow the fandom and can confirm that it currently works, other than the setstage (which I remember it used to work). I was able to successfully complete all the quests. I do have all the Patches in the game but maybe some other mod screw up with the quest again.
But anyway, people have options. Setstage didn't worked to me, fandom list of commands did.