|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|
Speak with Father
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 them to destroy the Railroad. If the player character refuses, Father will say it is an order. If the player character says they are not allies or has failed Tradecraft, there will be no option to warn Desdemona; when going to talk to her, she will say that the Railroad is aware of player character working with the Institute and asks them to leave, and the rest of the Railroad will be dismissive of them.
When arriving 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 the player character fires 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. 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 the player character attacks, he will likely be walking around the Commonwealth. He will have to be chased down 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. The player character is instructed to the speak with Doctor Li/Doctor Watson about this. End of the Line is completed and Airship Down begins. If the Prydwen was already destroyed in Rockets' Red Glare, then End of the Line is completed and Nuclear Family begins.
2. Siding with the Railroad - Warn Desdemona
To keep one's allegiance with the Railroad, they must inform Desdemona about the Institute's orders for the Railroad's execution. She will tell the player character to stall for time and continue working with Patriot. One will at that point need to do a long series of quests, starting with Underground Undercover, before End of the Line fails. There is no reward for this outcome, but the player character gets to remain a member of the Railroad. If all objectives have been completed for Underground Undercover prior to speaking with Z1-14 to advise that the rebel synths are ready to fight for their freedom, he discovers that the Brotherhood of Steel has found the Railroad HQ and asks the Sole Survivor to warn Desdemona as quickly as possible. Speaking to Desdemona will complete Underground Undercover and start Precipice of War.
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- Deacon will disband and turn hostile if the Railroad is attacked.
- If the player character has already eliminated the Railroad themselves or by completing 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, having hoped there would be alternatives.
- If Boston After Dark or a Railroad quest which involves certain characters being set to protected has not been completed, those characters may remain protected and may even follow you throughout the Commonwealth.
- If X6-88 is the current companion when approaching the Railroad HQ, the entire base will automatically turn hostile.
- Killing any named Railroad agents will make the player enemies with the Railroad.
- If Deacon is in a settlement during the quest, attacking him may make certain settlers become hostile.
- It is possible to hold off on the Railroad's destruction by warning Desdemona and continue with the Railroad questline. One can then destroy the Railroad after completing Rockets' Red Glare should they choose to remain with the Institute. This will net more XP in the long run. One also faces 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, the player character will get both objectives (Warn Desdemona and Kill Desdemona) at the same time. When speaking to Desdemona, one will have the option of telling her about both the impending BOS attack as well as the orders from the Institute to kill them. If one chooses to continue helping the Railroad, she will direct the player character to deal with the BOS first.
- Despite this quest being about destroying the Railroad, oddly enough the Ticonderoga building where High Rise and a large group of Railroad agents reside remains unaffected. If the player character has not completed Boston After Dark, the building is inaccessible.
- setstage Inst306 30 [verified] 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:
- 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 and 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] Quest won't progress - an alternate issue: If you warn
- 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] 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 be unable to proceed to
- 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. On PC, use tcl to toggle clipping off before using the glitch and then back on once through the wall.[verified] The player will be unable to access
- Predictive Analytic Machine to stop being hostile and continue giving quests for the Railroad.[verified] If you manage to kill all essential targets quick enough while sneaking it is possible for