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UPDATE: I realize Survival Mode disables the console and this will not work under normal conditions, if you really want to complete the quest (I did because during the last questline you can reveive a bobblehead in the asylum) my only suggestion to you is go to Nexus mods' website and download the mod to enable the console. 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 Speak to Jack about Arabia, then try to get more information from him.
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If you are still missing Emogene go to Cabot House and open the Command Console enter these codes: (This is how I did it)
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If you have the issue where Emogene is missing from behind the door at the Church you can fix it with this.
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