|Institute main quest: End of the Line|
|Speak with Father.|
|Kill Desdemona.||Inform Desdemona about the Institute's orders.|
|Leads to: Underground Undercover|
|Eliminate the Railroad leaders.|
|Speak to Father.||(Optional) The Brotherhood of Steel has already been eliminated.|
|Reward: 500 XP||Reward: 500 XP|
|Leads to: Airship Down||Leads to: Nuclear Family|
Detailed walkthrough Edit
Speak with Father Edit
Father will ask what the player character thinks of the Directorate's intention to destroy the Brotherhood of Steel. Even if the player character says that it is a mistake to do so, Father will insist that it is the only right decision because otherwise the Institute will be destroyed. He then reveals that the player character's involvement with the Railroad is known and asks whether they are ready to turn on the Railroad. Even if the player character says that they are allies and argues to save them, he wants you to destroy them. If the player character refuses, Father will say it is an order. If the player character says they are not allies, there will be no option to warn Desdemona; when you go to talk to her, she will simply ask you to leave and the rest of the Railroad will be dismissive of you.
Kill Desdemona Edit
When you arrive at Railroad HQ, the next step can be approached multiple ways, but will end in one of two results.
1. Siding with the Institute - Killing Desdemona
The moment you fire a shot at someone, everyone in the Railroad HQ will turn hostile. Glory is the biggest threat of the faction. She uses a minigun, and is equipped in heavy armor. It is recommended you focus on taking her out of the picture first before everyone turns their gun on you. The rest of the faction will use unmodded pistols, aside from Deacon who will use whatever weapon he has on him at the time. If Deacon isn't at HQ when you attack, he will likely be walking around the Commonwealth. He will have to be chased down for you to proceed with the mission. After killing the leaders of the Railroad return to Father. He tells about a plan to drive the Brotherhood of Steel out from the Commonwealth to discourage them from returning. This plan is about teaching the Brotherhood that the Institute at any time and place can turn their own technology against them. You are instructed to the speak with Doctor Li/Doctor Watson about this. The quest completes and the next starts.
2. Siding with the Railroad - Warn Desdemona
To keep your allegiance with the Railroad, you must inform Desdemona about the Institute's orders for the Railroad's execution. She will inform you to stall for time and continue working with Patriot. You will at that point need to do a long series of quests, starting with Underground Undercover, before End of the Line updates, and informs you that the quest failed. There is no reward for this outcome, but you get to remain a member of the Railroad.
- If the player character has already eliminated the Railroad with Tactical Thinking Father will only simply express relief that the Sole Survivor has already handled it, and complete the quest immediately. However he will also express regret, hoping there would be alternatives.
- If X6-88 is your companion when you approach the Railroad HQ, the entire base will automatically turn hostile, preventing the player from siding with the Railroad.
- Killing any named Railroad agents turns the entire faction hostile for the rest of the game, so one must tread carefully.
- It is possible to hold off on the Railroad's destruction by warning Desdemona, and continue with the Railroad questline. You can then destroy the Railroad after completing Rockets' Red Glare should you choose to remain with the Institute. This will net more XP in the long run. You also face less opposition since Glory is already dead.
- It is also possible to complete Underground Undercover before starting this quest. Since Underground Undercover only completes after Powering Up, which also begins End of the Line, you will get both objectives (Warn Desdemona and Kill Desdemona) at the same time. When speaking to Desdemona, you will have the option of telling her about both the impending BOS attack as well as your orders from the Institute to kill them. If you choose to continue helping the Railroad, she will direct you to deal with the BOS first.
- Deacon and Curie will love it if you choose to protect the Railroad.
- Piper, Hancock and Curie hate it if you destroy the Railroad.
- MacCready will like it if you choose to destroy the Railroad, and dislike it if you spare them. If the sarcastic option is chosen, you can spare them with no gain or loss in affinity with him.
- pc Quest won't progress on the (Eliminate the railroad leaders) stage even though all of them are killed. A fix is by completing the stage using the console: Setstage Inst306 30 [verified]
- pc Quest won't progress - an alternate issue: If you warn Desdemona about The Institute's plans, The Brotherhood of Steel begin to attack both the Sole Survivor and The Railroad. If at this point you change your mind and decide to kill both parties present (the Brotherhood of Steel and the The Railroad) you may not be able to kill Glory - oddly though she is not hostile towards the Sole Survivor - the fix for this is the same console command as the previous bug: Setstage Inst306 30 [verified]
- pc Quest won't progress - a third issue: If you've previously eliminated the Brotherhood of Steel presence on the Prydwen you'll be unable to warn Desdemona, and therefore unable to proceed to Rockets' Red Glare or The Nuclear Option (Railroad) if you want to play the Railroad's endgame. You can still end the game on friendly terms with the Railroad by getting Banished from the Institute and then completing The Nuclear Option (Minutemen).[verified]
- ps4 xboxone pc The player will be unable to access Railroad HQ where Desdemona is, if before siding with The Institute the player has already started the quest Tactical Thinking from the Brotherhood of Steel. The secret passage will be locked, and the player will not be able to interact with the mechanism to open it. This link  shows a glitch that breaks through the wall. For pc PC, use the console command tcl to toggle clipping off before using the glitch and then back on once through wall.[verified]