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Back at Railroad HQ Desdemona and Doctor Carrington can be found discussing a safe way to transport H2-22 after his memories were altered by Dr. Amari. P.A.M. will tell the group about increasing Institute activities, which will start a discussion between Desdemona and Carrington on how the Railroad should react. While Desdemona suggests rerouting the path, P.A.M. and Carrington will state that the safest way is to eliminate any synths blocking the original route.
After siding with one of the two parties, the Sole Survivor is sent to Dr. Amari to tell her about the new plan. After that conversation, Amari will tell the Sole Survivor to grab the Goodbye from H2-22 holotape from the table, which contains a personal message from H2-22 (although the conversation with Amari may take place elsewhere, "the table" in question is the round one with the red tablecloth behind Irma on the first floor stage).
The Survivor is then sent to Malden Center to eradicate any Gen 1 synths in the area. Before entering the station they run into Glory who was accidentally sent to accomplish the same mission. Together they destroy all synths, even though Glory constantly comments on the fact that she believes even Gen 1 synths should be rescued (e.g. asking if they couldn't just scare them away). It is also possible to dismiss Glory by saying you don't need any help when you first meet her outside of the station, in which case she will return to Railroad HQ, leaving you to clear the area yourself.
- Glory will be at the location where the synths are located, and will accompany the Sole Survivor through the mission. If Glory is dead, you can find her body there instead.
- If the player is in good standing with The Institute the synths won't attack the player. However, Glory is hostile against the synths, allowing the player to finish the quest without killing any synth. Killing synths in this quest won't make synths attack the player. This may not be the case if you dismissed Glory.
- If you find Doctor Amari downstairs, it may not be obvious where the holotape is. It's upstairs on a table next to the large stand up computer console behind Irma.
- It is possible to initiate this quest by simply clearing out Malden Center of synths and raiders. The quest will initiate from the quest marker 'Report back to Desdemona' once you kill the synth leader, whereupon you may go back to Railroad HQ. On arrival you will find Desdemona and Doctor Carrington discussing the situation, and the dialogue will proceed as if the quest was being given for the first time. However, Desdemona will have a quest marker above her head (if you have the quest active). At this point both her quest marker and 'Talk to Doctor Amari' will be active and you may either talk to her and complete the quest, OR you may ignore her/back out of dialogue and continue the quest as per the full quest markers, meeting Amari, the encounter with Glory, etc. The synths and a few of the raiders will respawn and you can repeat this stage of the quest, the only difference being that even when all the synths are dead you will still have both 'Report back to Desdemona' and 'Eliminate the Gen 1s' active. Talking to Desdemona will complete the quest as normal.
- Valentine, Hancock, Deacon, and Strong all like it if the player decides to team up with Glory to clear out the Malden Center; MacCready and Cait dislike it, but Cait and MacCready likes it if the player decides to dismiss Glory; Strong dislikes it.
- If cleared before the quest: the synths inside will respawn. The raiders and outside synths will still be dead. The elevator down to the synth leader will be still accessible.
- Glory is considered essential during this quest but that ends the moment the last synth is dead. If raiders are still alive, they can then kill Glory and you have to report her death to Desdemona. If she dies before you've completed Emergent Behavior, then an alternate caretaker takes her place.
- Desdemona says you've never met Amari, even if you're already completed Emergent Behavior and Glory or the alternate Railroad agent has seen you with her.
PC Desdemona does not have dialogue for reporting back to her if The Molecular Level is active and the stage where a supporting faction must be chosen has been reached, making it impossible to finish this quest until one proceeds in The Molecular Level. [verified]