Duty or Dishonor

Duty or Dishonor is a Brotherhood of Steel side quest in Fallout 4.

Detailed walkthrough
Talking to Captain Kells will start the assignment. He will ask the Sole Survivor to report to the logistics department and investigate a case of missing goods.

Knight Sergeant Gavil is the first contact and they will brusquely deny any accusations and direct the Sole Survivor to Knight Lucia and Initiate Clarke, since none of the other people in the department should be disturbed, also as the newest additions they are the most likely suspects.

The Sole Survivor now has multiple options:
 * Talking to Clarke and Lucia and passing speech checks. If the Sole Survivor speaks to Lucia first, then speaking to Clarke is unnecessary. To hear what both have to say, speak to Clarke first.
 * Return to the Prydwen's main deck. In the area where the personal beds with footlockers are, two of them - near the 'outgoing mail terminal' - have locked footlockers belonging to Clarke and Lucia. Inside Clarke's is a note from Lucia and a key to Lucia's footlocker, while in hers - is a holotape. There are four logs on it, but the fourth one is important. After confronting Lucia she will ask the Sole Survivor to tail Clarke after his shift ends to find out what's wrong.
 * Alternatively, the Sole Survivor can search the depot room for clues, and look for the terminal next to where they met Gavil. This will also advance the quest.

Shadowing Clarke will lead the Sole Survivor to the Boston Airport ruins. Upon entering the ruins, the Sole Survivor must find Clarke. Go to the right from the elevators that require an ID card, open the door, and head down the stairs and through a tunnel. In a room to the left, the body of Knight Rylan can be found. Killing ghouls on the way to Clarke will not cause him to be hostile; killing the ones where Clarke is found, however, will make him hostile. Further down the tunnel, the Sole Survivor will be tasked with the optional quest to exterminate the ghouls. At the end of the flooded tunnel blocked by a gate, the Sole Survivor must go up the ramp on the right and through the stairwell/tunnel until one gets to an underground parking garage. Traverse the underground parking garage until arriving at a subway tunnel. Take the subway tunnel until one gets to the next platform, which will lead to a luggage terminal.

Upon entering, take the stairs down and follow this tunnel until arriving at a room that Clarke is in, which is above the generator room with a bunch of ghouls. Opening the generator room and killing the ghouls will cause Clarke to automatically become hostile forcing the Sole Survivor to kill him. Similarly, entering the next room adjacent to the room Clarke is in without talking to him will cause him to become hostile.

The ID card is on the desk that has the [expert] terminal. This is needed to open the doors and use the elevators. Another ID card is available from Clarke. If no ghouls were killed and the Sole Survivor has settled on confronting Clarke directly, there are four options:


 * Convincing Clarke to turn himself in grants a piece of armor upon quest completion (T-60c torso with 10% AP costs in VATS reduced as well as leveled options). The optional quest objective of killing the ghouls is also automatically completed.
 * Convincing Clarke to leave the Brotherhood of Steel, after which one can either lie to Kells about the missing food or blame it on Clarke. Kells will be doubtful of the Sole Survivor's words at first, but he will be convinced after they continue with the lie. This option grants 50 caps and some experience.
 * Kill Clarke, but this will yield no armor or weapon rewards, just 100 caps.
 * Keep Clarke's secret and lie to Captain Kells about the thief's identity.

Upon completion, Kells will give the Sole Survivor one of several rewards depending on what happened to Clarke. Only by convincing the traitor to turn himself in will Kells give the Sole Survivor the Exemplar's T-60c torso. (Note: While the armor is titled T-60c, it is leveled to the player character, meaning higher level player characters will receive T-60d, e, or f, while lower levels will receive a, b, or c.)

After the mission is complete, one can speak with Kells. Even though he states that a patrol team was sent in to clear out the ghouls, the room at the bottom of the ruins will still be populated by them.

Bugs

 * If Clarke spots the player character, he may get stuck in an infinite loop of going inside and back outside again. If there is a companion in the party, this can be fixed by ordering them to wait elsewhere, which should trigger Clarke to run. It is also possible to run ahead and hide in the bushes by the broken down plane and he will continue his walk.
 * If one enters the underground Boston Airport ruins for the first time while wearing power armor equipped with the Targeting HUD mod or use Berry Mentats while inside, the quest will glitch. Clarke will not initiate conversation as he is supposed to and will always be hostile. Reloading to a previous save and entering without the Targeting HUD equipped prevents this issue. However, equipping the mod or using Berry Mentats will reactivate the bug.
 * If Clarke is hostile, it is still possible to progress through the entire conversation by repeatedly using Pax syringe on him. Unfortunately, even if he is convinced to turn himself in this manner, the quest will not advance beyond "Kill Initiate Clarke."
 * When shadowing Initiate Clarke, he may not proceed any further than a certain point. If he is killed by placing a live grenade in his inventory, then the quest icon still appears above his corpse as if he is alive, but the key to the Boston Airport ruins can be looted, followed by an update telling the player character to kill Initiate Clarke. However, this does not fix the quest as Initiate Clarke is already dead and therefore the player character is unable to kill him again.
 * If the Sole Survivor killed the ghouls before speaking to Captain Kells and thus entering the Boston Airport ruins before getting Duty or Dishonor, and thus setting stage 380 "Kill Initiate Clarke:" after leaving the Airport Ruins there is no way to return to where Clarke is (behind the entry door in the ruins) after speaking with Captain Kells, without console commands, as the door is locked and can only be opened with a key from Clarke. And Clarke will not exit the ruins. Clarke will not appear in the game until after speaking with Captain Kells.
 * If the Sole Survivor has found out the evidence of From Lucia note but did not confront her before proceeding to shadow Clarke and instead do it after, the quest marker 'Confront Lucia' will be stuck on Lucia, and the Sole Survivor won't be able to trigger the quest dialogue with her. However, when the Sole Survivor reports to Captain Kells the quest marker will automatically be marked as completed.
 * If the Sole Survivor has already completed the main quest for a different faction, destroyed the Prydwen, and then uses a jetpack on the elevator to reach the second floor door and the out of bounds area, they can get the card key off the desk and open the door to the reactor room. It will start the "Duty or Dishonor" quest at the "Kill Initiate Clarke" stage and will not be able to be completed.
 * If one enters the airport ruins before encountering the Brotherhood and unlocks the room containing the ghouls (with the employee ID found on the table), it will automatically start the quest. This locks the entrance door, sealing the player character inside without access to the key.