Underground Undercover

Underground Undercover is a Railroad main quest and an achievement/trophy in Fallout 4.

Detailed walkthrough
After the Sole Survivor gets into The Institute, The Railroad wants them to make contact with an anonymous person inside, nicknamed Patriot, that's been helping synths escape. Tinker Tom provides the encrypted message holotape that will upload a message for Patriot to the Institute's network in the hopes that Patriot sees it and comes forward to identify themselves.

After uploading the message, Patriot sends a message back telling the Sole Survivor to meet him in a maintenance closet. Patriot turns out to be Liam Binet, an institute scientist and son of Alan Binet, the head of the Robotics department. Liam expresses surprise that anyone decoded the messages he was sending out with each synth he freed and were then able to contact him back, and he is excited at the prospect of coordinating with The Railroad.

He introduces the Sole Survivor to a synth named Z1-14 who has been working with him to help synths escape. They discuss how many synths are ready to leave and propose a plan to free all thirteen at once with the Sole Survivor's help. To escape, Liam will need to bypass SRB electronic security to open some doors, but he isn't able to crack it. Instead, he requests a pre-War admin password from the surface. He recommends asking The Railroad for any leads on where to find one. It should be noted that the player must complete the quest Institutionalized at this point in order to be able to leave the Institute compound.

The Sole Survivor returns to Desdemona at Railroad HQ and is instructed to enter their mission report in the terminal in P.A.M.'s office. P.A.M. analyzes the data and recommends that the login credentials for Wilfred Bergman may be found in Cambridge Polymer Labs. Desdemona instructs the Sole Survivor to retrieve it while they consider Liam's plan.

The password can be found in the laboratory section of the building on the second floor. In order to access it, however, the quest Cambridge Polymer Labs must be completed before escape from the building is possible.

Looking over Liam's plan, Desdemona concludes that if it is successful, it may never be possible for Liam to free another synth ever again due to the Institute going on high-alert following such a security breach. She proposes instead that they should use this opportunity to free every synth in the Institute. To do that would require the synths themselves to rise up and fight for their freedom, instead of operating in the shadows. She instructs the Sole Survivor to give Liam the password he requested, but then to cut him loose and coordinate with Z1-14 instead from then on.

Back in the Institute, the Sole Survivor gives Liam the password, then meets with Z1-14 to discuss Desdemona's proposal. He agrees with the plan and asks for 24 hours to ensure that it is possible. He speaks with the other synths and is surprised at how many volunteers he receives. They will need weapons, however, so he requests that the Sole Survivor aids them by killing a few guards so they can stage a construction accident, allowing a few synths to go into hiding in order to construct weapons. The Sole Survivor may optionally offer to provide additional weapons, which Z1-14 instructs to be placed in a maintenance closet.

The guards are in a maintenance tunnel between Synth Retention and Robotics. After they are dispatched, the worker synths will give their thanks and collapse the tunnel after the Sole Survivor departs. Speaking with Z1-14, he gives his thanks as well and states that they need time to prepare. In the meantime, the Sole Survivor should keep working with Father until they are ready. At this point the quest is put on hold until Powering Up is completed.

After meeting with the Directorate, a runner will arrive in the meeting room with a message from Z1-14 that the Sole Survivor's quarters have flooded and they are needed there immediately. When they arrive, Z1-14 states that he's discovered the Brotherhood of Steel are moving to attack Railroad HQ and The Railroad needs to be warned as soon as possible.

Bugs

 * | Sometimes Liam won't move after telling the Player to follow him. Player cannot talk to Z1-14 when Liam is stuck in the storage room. To solve this, go to Z1-14, then use the console command.
 * | Sometimes the 'Continue Working With Father' objective never ends, even past Mass Fusion and Powering Up. Can use the console command  or alternatively you can use the command  to move past this glitch. Talking to Liam Binet could also trigger a runner to come get you on Z1-14's behalf.
 * | Sometimes the encrypted message holotape will not be added to your inventory. A console fix for this is:  Possibly because player teleports before quest item is given to player and player continues quest with network scanner holotape which for some reason contains quest related data to be uploaded for undercover agent.
 * | Should Tinker Tom get downed in combat with other NPCs prior to the player securing the vertibird, Tom may remain incapacitated by the entrance door to each new area the player spawns into. The player will not be able to revive him with a stimpak, and as such he will not be able to fly the vertibird, effectively bringing the quest to a complete halt.
 * | When prompted to kill the tunnel guards, only 4 of the 5 guards spawn. This results in the 5th guard marker spawning beneath the floor.
 * | It is possible that Desdemona will not initiate dialogue when trying to warn her about the brotherhood.
 * PC beta patch 1.3 resolves this issue in at least some cases.
 * This may be caused by Glory being dead. To fix go to Railroad HQ and use and  in the console. You can also fix by  followed by  and finally  This must be done before Z1-14 informs the Sole Survivor of the impending Brotherhood attack.
 * | It is possible that during and after Glory assists the player during the quest Memory Interrupted she can either become stuck in the area or die, resulting in a halt to progress for Underground Undercover. This is because Glory is involved in a dialogue with the player during the Brotherhood of Steel warning event. To avoid this, the player should follow Glory out of the Malden Center Station as she can become stuck on metro gates or other objects.
 * If Deacon is dead, this can also cause the same issue.
 * The quest can be force completed by using either the command or  at the Railroad HQ. However, this will not initiate the next quest, Precipice of War. This method is only effective if a way to force start the next quest is available.
 * This may be caused by Brotherhood important NPCs being dead. To fix use recycleactor in the console for every dead body left in the Prydwen, Boston Airport, and Cambridge Police Station. It is uncertain though who exactly causes this. This must be done before Z1-14 informs the Sole Survivor of the impending Brotherhood attack.
 * This bug can also occur if the player character has not killed any members of the Brotherhood of Steel in the Prydwen, Boston Airport, or the Cambridge Police Station, or if Glory is still alive.
 * | If "Warn Desdemona" is active and the Brotherhood didn't become hostile during Mass Fusion, either by activating the fast travel point manually and thus skipping the confrontation or by using the console to bypass that stage of the quest, the NPCs on the Prydwen will talk to the Sole Survivor as if the assault on the Railroad had already taken place and failed.
 * | Desdemona is always busy. When Z1-14 warns the Survivor of the incoming attack on Railroad HQ, don't leave the Institute immediately and don't teleport into Railroad HQ. Talk to Father first, then take the elevator up to the Institute, beaming out to the Old North Church, not HQ. From there walk slowly through the catacombs and just outside HQ, Glory will be standing there with a minigun saying she's on her way out for a mission. Go into HQ and your character will initiate the warning automatically.
 * | If you Meet Father, but refuse to join him, You will be ejected and forced to use the Railroad to get into the Institute.  This is suggested by Desdemona as the only remaining option.  However after the Institute is destroyed by the Minutemen Railroad actions will be confusing.   They will act as though Glory had been killed, saying "Without Glory..." and other such lines.   Her death happens on the full Railroad quest line, but didn't happen here.  Glory will still be walking around the HQ, but will remain silent and not react with you or anyone else.  She just "haunts" the HQ.

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