Emogene Takes a Lover

Emogene Takes a Lover is a side quest in Fallout 4.

Detailed walkthrough
Immediately upon completion of Special Delivery, Edward Deegan requests that the Sole Survivor help find Emogene Cabot, who is apparently prone to running off with new boyfriends over the objections of Jack. Edward informs the Sole Survivor that Emogene likes to spend time in Goodneighbor at the Third Rail.

Talking to the bartender at the Third Rail results in being pointed to Magnolia, talking to her results in the player getting a flyer from Ham pointing the way to Brother Thomas, a cult leader that seems to have recruited Emogene. If the player chooses the aggressive dialogue option Magnolia will not tell them where Emogene is, but choosing any other of the others will get her to reveal the location.

Thomas is found at the Charles View Amphitheater, 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 Emogene free.

Once Emogene is free she will reveal the truth about the purpose of the serum, then leave on her own. The player can go back to Cabot House and turn in the quest. On arrival, Jack is talking to Edward over a ham radio, who is defending Parsons State Insane Asylum from raiders. After a few minutes, the radio dies and Jack decides to head to the asylum with the Sole Survivor to try to stop the raiders, starting the quest The Secret of Cabot House.

Bugs
Brother Thomas unlocks the door to where Emogene is supposed to be but she does not appear. Instead the quest points back to Cabot House and the locked section of the house. On PC this bug can be fixed using console commands, however on PS4 and Xbox One there is no confirmed fix.
 * 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:, , , ,
 * Alternatively (and preferably), one can restore the conversation with Emogene by typing the following commands, , , , , 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.