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 you to report to the logistics department and investigate a case of missing goods over the last time.

Your first contact will be Knight Sergeant Gavil, who will brusquely deny any accusations and tell you to only bother 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.

You now have multiple options:
 * Talking to Clarke and Lucia and passing speech checks.
 * 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. Confront Lucia and she'll ask you to tail Clarke after his shift ends to find out what's wrong.
 * Alternatively, you can search the depot room for clues, and look for the terminal next to where you met Gavil. This will also advance the quest.

Either way you end up following Clarke.

Shadowing Clarke will lead you to the Boston Airport Ruins. Upon entering the ruins, you are tasked with finding Clarke. Go to the right from the elevators that requires an ID card, open the door and down the stairs and through a tunnel. In a room to the left is the body of Knight Rylan. Killing ghouls on the way to Clarke is OK. Further down the tunnel you'll be tasked with the optional quest to exterminate the ghouls. At the end where the tunnel is flooded, go up the ramp and through the stairwell/tunnel until you get to an underground parking garage. Traverse the underground parking garage until you get to a subway tunnel. Take the subway tunnel until you get to the next platform, this will lead you to a luggage terminal.

Upon entering, take the stairs down, follow this tunnel until you get to a room that Clarke is in, that's above the generator room with a bunch of ghouls. If you open the generator room and kill the ghouls Clarke will automatically become hostile forcing you to kill him. Also, if you go into the next room adjacent to the room Clarke is in without talking to him, Clarke will automatically become hostile.

The ID card is on the desk that has the [expert] terminal. You need this to open the doors and use the elevators. Another ID card is available from Clarke. If you did NOT kill the ghouls and have settled on confronting Clarke directly, you now have three 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.
 * You can convince Clarke to leave the Brotherhood of Steel, after which you can either lie to Kells about the missing food or blame it on Clarke. Kells will be doubtful of your words at first, but he will be convinced after you continue with the lie. This option grants 50 caps and some experience.
 * You can outright kill Clarke, but this will yield no armor or weapon rewards, just 100 caps.

Upon completion Kells will give you one of several rewards depending on your what you did with Clarke. Only by convincing the traitor to turn himself in will Kells give you the Exemplar's T-60c Torso. (Note: While the armor is titled 60c, it is actually 60b.)

After the mission is complete, you 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. You can enter, kill, and loot to your heart's content (if Clarke turned himself in).

Bugs

 * If Clarke spots you he may get stuck in an infinite loop of going inside and back outside again. If you have a follower, this can be fixed by ordering them to wait elsewhere, which should trigger Clarke to run. You can also run ahead and hide in the bushes by the broken down plane and he will continue his walk.
 * If you kill Clarke by placing a live grenade in his inventory after you promise not to turn him in it may cause the game to register that he is not dead forcing you to reload past save date.
 * If you enter 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 in this manner, the quest will not advance beyond 'Kill Initiate Clarke'.
 * When you shadow Initiate Clarke he does not proceed any further. If you kill him by placing a live grenade in his inventory then the quest icon still appears above his corpse as if he is alive, but you can loot the key to the Boston Airport Ruins and get an update telling you to kill Initiate Clarke, however this does not fix the quest as Initiate Clarke is already a corpse and unable to kill him again.