End of the Line

End of the Line is a quest in Fallout 4.

Quick walkthrough
The quest is started automatically upon the completion of Powering Up.
 * 1) Speak with Father
 * 2) Kill Desdemona
 * 3) Eliminate the Railroad leaders

Detailed walkthrough
Father will ask what you think of the Directorate's intention to destroy the Brotherhood of Steel. Even if you say 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 informs you that your involvement with the Railroad is known and asks if you are ready to turn on The Railroad. Even if you say that they are your allies and argue to save them he wants you to destory them. If you refuse, he will say 'it is an order'.

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 Dr Li 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 Institutes 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 quest, starting at 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.

Bugs

 * 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: