THE RAILROAD QUEST 03 - Underground Undercover
Triggered by using The Railroad to help you build the signal interceptor during Story 10 - The Molecular Level. Just before teleporting into the Institute Desdemona will give you a tape which begins the quest.
Objective: Upload encrypted message on any Institute terminal
After Desdemona hands over the tape and tells you about Patriot and you teleport to the Institute, you'll arrive in the relay chamber on the upper level of the place. The earliest terminal you can use is directly in front of you when you arrive, just through the door. Interact with the terminal and insert the network scanner holotape.
Three options will appear when the tape loads. You can read the explanation from Tinker Tom if you like but it isn't necessary. Initiate a network scan (this will be required if you make an enemy of the Institute later so you can regain access through the Minutemen quest line). Then copy the encrypted message.
Objective: Read Patriot's reply
A couple of seconds later, a reply will appear in the list of commands. Pick that option.
Objective: Meet Patriot
Patriot's response will tell you to meet him in the Advanced Systems maintenence room. However, you are going to need to pass through some of the events in Story 11 - Institutionalized (avoiding spoilers here) before you can access that location. When you descend in the main lift to the center of the Institute, follow the marker through the maze of rooms until you reach the maintenence room where Patriot is waiting.
Objective: Follow Liam
Have a chat with him and talk to him about The Railroad. After he gives you some info about his plan, he'll lead you to one of his comrades. A synth by the name of Z1-14 who seems to be the real brains of the operation. After a quick chat about their plans, Liam will want to talk to you.
Objective: Talk to Liam
Liam requires you to track down some login credentials in order for him to help with the plan. He thinks some old terminals on the surface could still hold those credentials. Off we go to visit Desdemona to find them.
Objective: Talk to Desdemona
Desdemona will want you to write up a report so they can analyze the information you've discovered.
Objective: Enter report on terminal
In the room PAM resides in you can enter the information you gleaned from the Institute on the terminal there.
Objective: Talk with PAM
After entering the report, turn around and talk to PAM about it. She'll give you the most likely location for finding the credentials if they still exist.
Objective: Get password for code defender
To find the password, you'll need to travel to Cambridge Polymer Labs. You will need to access the laboratory area (through the broken decontamination room) at the back of the building and enter an office on the second level to find the terminal. For a more detailed description and walkthrough you can read Sidequest - Cambridge Polymer Labs. Completing this sidequest properly also earns you a piece of high end legendary power armour (torso), so it is well worth the time. After obtaining the password, return to Railroad headquarters.
Objective: Return to Desdemona
When you converse with Desdemona, she will give you an alternate take on the current plan. After giving you some advice, you'll be heading back to the Institute to inform your two partners in synth liberation.
Objective: Give password to Liam Bennet
When you arrive, talk to Liam and hand over the password. Moving on.
Objective: Meet with Z1-14
Talk to Z1-14 about your new and improved plan. After hearing about the changes, he'll agree and ask for a bit of time to prepare.
Objective: Give Z1-14 a day
Sit down on a nearby seat and wait for 24 hours.
Objective: Meet with Z1-14
Z1-14 will inform you that the main problem at the moment is a lack of weaponry for him and his fellow synths. Several crates in the tunnels under the Institute contain components that could be used to manufacture weaponry, but the area is under guard. As expected you're going to have to clear the way for the synths working there to capture those crates.
Objective: Kill the tunnel guards
Follow the marker to a nearby elevator that leads down to the tunnels below. The guards will all be marked so they are easy to spot. Keep in mind they will be wearing synth armour which can make them tough to bring down on higher difficulties (use energy weapons against them as they are slightly weaker to them). The good news is that when you begin the attack on any guard the other synths in the area will rise up and attack them. This means you can simply start the fight and then hole up in a corner protected by mines or snipe at the guards while they are surrounded by melee synths. Don't think you need to take on the guards all by yourself.
Objective: Return to Z1-14
Once the guards are all taken care of and the synths are gone, return to the main area of the Institute above and have a chat with Z1-14 to tell him the good news.
Objective: Continue working with Father
From this point onwards, you'll need to complete several quests for the Institute before you will be contacted again. You will need to complete all numbered Institute quests until you finish The Institute 06 - Powering Up.
Note: You can trigger The Railroad 04 - Operation Ticonderoga by talking to Desdemona at any time after completing Story 11 - Institutionalized, but before starting The Railroad 05 - Precipice Of War.
At the end of the meeting when Powering Up ends, a synth will arrive with an urgent message.
Objective: Meet with Z1-14
Return to your quarters to find Z1-14 waiting for you. He'll inform you that the Brotherhood has located The Railroad's headquarters and is about to launch an attack. The race is on to warn The Railroad before they are wiped out.
Objective: Warn Desdemona
When you materialize within the Railroad headquarters, rush over and warn Desdemona. She'll hand over the vicious railway rifle that fires railway spikes at opponents for high damage (180 per shot in my case). She'll also hand over a couple of hundred spikes for you to use as the Brotherhood breaches the headquarters. This will trigger the next quest The Railroad 05 - Precipice of War and finally end this extremely long quest.