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So annoying
It's not hard to reset a quest stage.
SetStage <QuestID> <Quest stage number>
http://fallout.wikia.com/wiki/Emogene_Takes_a_Lover
http://fallout.wikia.com/wiki/Fallout_4_console_commands
Edit: If all else fails use the CompleteAllQuestObjectives command to finish the quest so you can proceed with the Cabot missions. Talking to her and then Jack are the last stages of that quest.
Edit 2: That is a verified bug according to the wiki. Look at the first link above for specific commands to complete it.
That will not work on the Cabot quest line. It will force completion of the 2nd quest but it will not set the stages for the third quest.
The problem with the quest line is quest #1 sets the stages for quest #2 and quest #2 sets stages for quest #3 and if one bugs out then next is bugged.
I think if you chase down Jack in quest #1 (after you first talk to him) and ask about Arabia that sets the stage right for the the 2nd one and Emogene appears where she needs to be.
Your best option is when doing the quests on a 2nd game make sure you have a good save before startign the first, then do the first and second back to back. The third only gets buggy if you didnt use the right console commands fixing the 2nd quest.
If you use a setstage command, make sure to zone out use the set stage, then zone back in, it helps a lot. Some stages wont set properly if you are in the cell when you change it.
setstage 000503B9 70
setstage 00022A00 705
setstage 00022A00 710
setstage 00022A00 720
setstage 00022A00 750
You will loose your serum tho, so might want to add that with commands to get it back.
Guess I'll have to use the console to complete this quest.
You are on PC right? Just download a mod to use console commands on survival.
Furthermore download "Fallout 4 script extender (F4SE)" and the mod that allows you to get achivement even with mods enabled (requires F4SE as a launcher).
I had to do this because Bethesda.
Hope i could help you out.. Anyway you should REALLY check the water around that location.. maybe she's underwater, but you still would not be able to talk to her in that case
Dont bother. Brahminshit theory. Using a console command that moves you to her location proves that one wrong.
If you want to avoid the bug then you need to talk to Jack and make sure to ask about Arabia during the first quest. When you skip that because you done it before in another game is when you start bugging out the quest because it fails to set the stage.
Of course I said this almost a year ago and have not had it bug out on me yet. Amazing how people dont pay attention.
Your choices are either Console commands (I don't know the ones in particular that will fix this) or to reload a save BEFORE YOU MEET EDWARD DEGAN.
It sounds to me like you got stuck in the worst iteration of the Emogene Takes a Lover Quest. The one that happens if you fail the dialog check when first meeting Edward. The quest seems to proceed fine, but ti script links to a dead end that never moves Emogene out of Cabot House.