Tradecraft

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

Detailed walkthrough
The quest begins immediately after completing Road to Freedom. The conversation with Deacon will change depending on the answer to Desdemona's question, if the Sole Survivor would risk their life for a synth.
 * If saying yes, Deacon will joke about "considering it a close personal favor" if the Sole Survivor didn't sell them out to the Institute, after which he will provide details on the job.
 * If saying no, Deacon will ask if the player character would at least help take the fight to the Institute for their crimes against the Commonwealth. Saying yes to this will lead to Deacon providing details on the job.

Either way, Deacon has an angle for getting past the usual, year-long procedure of becoming a Railroad agent, suggesting a two-man mission to the Railroad's former hideout in Lexington. Meet him on the city's outskirts to continue the mission.

Outside Lexington, Deacon provides more details on the job, as well as introduces the player character to a few railsigns, and gives the player character a countersign ("Mine is in the shop") to use with Ricky Dalton, a tourist they're about to meet. They rendezvous with Ricky, who asks the Railroad's sign "Do you have a geiger counter?" The player character can use the countersign or not, afterwards Ricky explains that the Slocum's Joe is crawling with Gen-1 synths.
 * Optional: The player character can persuade Ricky for additional aid: an easy Charisma check to get extra supplies, a medium check to provide sniper fire when the violence starts, or a hard check to provide an explosive distraction. Ricky notes that the distraction will likely kill him, at which point the player character can still tell him not to do it and he will resort to providing sniper fire instead. Note that failing any persuasion attempt will cut off all others, and passing the medium or hard before the easy check will cut off that option as well. If persuaded to do an explosive distraction, Ricky will walk to near the Slocum's Joe and sit on a large rock and do nothing more. He is highly likely to be attacked by mongrel dogs or Gunners on the way and die.

Option 1: Frontal assault
Proceed to the Slocum's Joe front entrance and begin a frontal assault. You will also need to circumvent or disarm all of the mines littering the front of the shop. Once inside, however, Deacon will give you the location of the hidden elevator only to realize it has been powered down, forcing you to use Option 2, sneaking in through the escape tunnel. (However, before update 1.4 it is still possible to enter this way by opening the elevator doors, jumping down the shaft, entering the elevator box via the hatch at its top, and opening the doors at the bottom. Careful of the mines in the hallway though.)

Option 2: Escape tunnel
Go back to where the Sole Survivor met Deacon and head to the quest marker, a sewer tunnel covered by a thick drape of moss. Upon entering the tunnel, the player character is given a little more information about the Railroad and the target. Shortly after the talk, Deacon will unlock the terminal with a few passwords he remembers.

Past the door, Deacon will point out a railsign signifying that there's a cache nearby. (It's in the back of the tube directly behind the sign.) Around here, Deacon will warn to just run if meeting a Courser (provided the player character hasn't previously fought one in the Hunter/Hunted quest). Ahead, there will be an unlocked terminal, which one can use to turn off the spotlights and turrets. Below is a group of synthetic that need to be passed. Once past this group, one can turn on the defenses that will start firing immediately against the next group of synths. Shortly after that, one will find out that the Railroad was using an old Defense Intelligence Agency site as their HQ.

The terminal next to the door leading out of this office area can turn off the tripwires in the next room. Before leaving, grab the fusion core in the room left of where the Sole Survivor first entered and a U.S. Covert Operations Manual on a desk in the room up the stairs.
 * If going right, there's some bathrooms with a synth and a locked door with some loot. After that, go left to continue the mission. Down the hall the player character will hit an intersection; left leads to the mission marker, right to the "databanks," and straight to the front door where the player character would have arrived otherwise. Upon entering the vault with the prototype, the player character will receive from Deacon a unique weapon, the Deliverer. A terminal controls access to two locked areas containing minor loot.

Once entering the last room before the marker, Deacon will open the vault and inspect a dead body. There are two hazmat suits and a bottlecap mine in the room before the vault, opposite a weapons workbench. After the inspection, he'll offer the "hand cannon" the dead man used and won't take no for an answer. In the vault, grab Carrington's prototype, the two Stealth Boys, the mini nuke and head towards the elevator. Before the player character leaves, to the right of the small set of stairs leading to the elevator is a locked door with an advanced lock where the player character can find another fusion core.
 * When topside, if haven't done so yet, the player character will have to destroy the synths and turrets that the Institute have stationed in the Slocum's Joe (unless the player character remains undetected and fast travel), and then deal with the mines on the way out. If Ricky is helping, there's a good chance he'll be killed providing sniper fire, although he can be saved, but guaranteed to die with the explosive mini-nuke distraction, which wipes out most of the synths.

Once back to the church, the Sole Survivor find Deacon embellishing their exploits to Desdemona. The Sole Survivor have the option to tell the truth or pass an easy persuasion check to go along with the lie. Either way, she's impressed with resourcefulness and extends an invitation to join the Railroad. Refusing leaves the offer open, but accepting leads to selecting a code name (or letting Desdemona pick 'Wanderer' after refusing a name twice) and completion of the quest, with Deacon becoming available as a companion.

Companion reactions

 * Curie likes it if the player declines the gun.
 * Cait dislikes it if the player declines the gun or tells Desdemona the truth.
 * MacCready likes it if the player goes along with Deacon's lie.
 * Piper, Preston Garvey, Nick Valentine, Codsworth, and Curie dislike it if the player goes along with Deacon's lie.
 * Piper and Hancock will dislike telling Ricky to make the distraction.
 * Deacon loves it when the Sole Survivor joins the Railroad.
 * Piper and Curie like it when joining the Railroad.
 * Danse hates it when joining the Railroad.
 * Curie dislikes if player lies to Desdemona.
 * Nick Valentine like it when choosing the nickname "Whisper".

Bugs

 * When you reach the stop under the Old Highway near Lexington, Deacon might get bugged and repeat the same lines and won't allow for dialogue to progress the the quest. To resolve this, simply reload a save or dying can allow him to initiate the proper response.
 * Deacon might stall in the hallway outside the room containing the locked vault and the inaccessible terminal. This can be prevented by following and clearing the dialogue tree at the start of the tunnel. To resolve the issue:
 * Save and reload the game, and optionally attack and down Deacon before doing so.
 * Exit the Switchboard via the Elevator and exit to the Commonwealth, upon re-entering the Switchboard via the elevator the vault should now be accessible.
 * While facing the door use console command to unlock the door:
 * Deacon might stall upon first entering the Switchboard, failing to move upstairs to access the terminal and unlock the double-doors (an issue if the player character doesn't have the Hacker perk). Open the console and left-click Deacon. Close the console and go stand directly in front of the locked doors. Open the console and type . The door should automatically open once Deacon is within close proximity.
 * When approaching The Old North Church to meet Deacon after getting Carrington's prototype, Deacon may suddenly move to the middle of the map making it impossible to meet with him. Loading a save game from the 'Get Carrington's prototype' step may solve this. Returning to the Switchboard to find and speak to Deacon there may also solve this.
 * The prototype may not be removed from the inventory after handing it over to Carrington. Talking to him a second time or, on PC, using may fix this issue.
 * Deacon might get stuck in mid air, unable to speak or move, after the player character has talked to him under the old highway. A way to fix this would be to target him, open the console, and type . This will fix Deacon floating around.
 * If you didn't talk to Deacon after entering the back entrance and only speaking to him after obtaining Carrington's prototype, the quest log will prompt you to get the prototype even when it's already in your inventory. And the quest log won't update even after the completion.
 * Regardless of if the speech check with Desdemona at the end of the quest is passed, she will say the same thing.

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