THE INSTITUTE QUEST 07 – End of the Line
Triggered by completing The Institute quest 06 – Powering Up
Note: DO NOT undertake this quest if you want to side with The Railroad. Attacking members of The Railroad will make the faction (obviously) hostile to you, failing The Railroad Quest 03 – Underground Undercover.
Note: If you want to complete The Railroad Quest 03 – Underground Undercover, you must talk to the synth who has a message for you from Z1-14 as you leave the directorate meeting and continue on with the Railroad quest's objectives.
Objective: Speak with Father
When you find and talk to Father, he'll inform you that The Institute plans to take steps to wipe out The Railroad once and for all with you leading the charge. Looks like The Institute has finally taken off the kiddie gloves with The Railroad and it's going to start pummeling.
Note: Don't have Deacon as your companion during this quest. Place him in a settlement (such as Sanctuary) and remove all his gear. This will allow you to kill him easily as part of a later objective. Leave him tooled up and in power armour and he'll make mincemeat of you on higher difficulties.
Objective: Kill Desdemona
Travel to the headquarters with your best weaponry (they don't have power armour which makes things easier) and position yourself well before starting the firefight, as Desdemona is in the middle of the main area of the headquarters surrounded by several Railroad personnel. Use one of the side tunnels with nobody nearby. You should be able to bring Desdemona down in a couple of seconds before the other Railroad members realize what's going on.
Objective: Eliminate the Railroad leaders
Your next concern will likely be PAM the assaultron and/ or Glory with her minigun. The other members pose little threat but these two can be deadly. Use cover to your advantage here and lob grenades into the cluster of enemies or use ranged weapons to pick them off from your superior position. If you're having real trouble, a well placed mini-nuke from a fatman can make them real peaceful, real fast. When the headquarters is clear, you'll need to return to the settlement with Deacon in it and dispose of him as well to complete this objective. This should be easy if you took my advice and disarmed him earlier.
Objective: Speak with Father
After the massacre is over, return to the Institute and tell Father that the job is done. Or so you thought as The Institute Quest 08 – Airship down begins and this one ends.