Duty or Dishonor

First you must complete “The Lost Patrol”. If you have already completed it, talk to Kells and tell him about Paladin Brandis. He'll give you a new suit of armor for completing this and will start this quest immediately afterward.

Go to the Boston Airport and find Gavil. Next, find Initiate Clarke and talk to him. Next, talk to Lucia in the same area. Ask her about the logistics and you can aske her about Clarke with two Charisma speech checks. If you passed this, she'll ask you to shadow Clarke. Otherwise, you have to check Lucia's logs in the crew quarters of the Prydwen.

Once done, you'll have to shadow Clarke as he leaves his post. This will Lead you to the Boston Airport Ruins. Once inside, from the elevator requiring an ID card, go to the right and open the double-door. You'll get the optional objective to exterminate the ghouls. The collapsed hall to the left has the body of Knight Rylan.

Continue to the end of the flooded tunnel and go up using the collapsed ceiling leading to the parking garage. There are a lot of ghouls here so use the explosive cars to take out these ghouls in the explosion. Continue going down the ruins. You'll find the Subway entrance near the elevators to the north.

Enter the subway and kill the ghouls along the way. Continue in the end of the tunnel which will Lead you to the luggage claiming area. Clear more ghouls here and find the stairs to the NE to reach the lower area where you can find Clarke feeding the ghouls. If you kill the ghouls he's feeding, Clarke will also turn hostile, forcing you to kill him. If you kept your trigger fingers with you, you can confront Clarke and learn his reasons. Even if you don't attack the ghouls, your companions will.

After talking to Clarke, you can convince him to turn himself via Charisma speech check. Once resolved, you'll get the employee ID card, which will allow you to use the elevator. There's also an Expert facilities terminal on the desk which can activate the two protectrons in the ghouls' holding cell. If you did this, the protectrons will attack the ghouls and will turn Clarke to a hostile.

Once you're done with Clarke, use the elevator to reach the upper floor then leave the area. Report to Kells to complete the investigation. If you convinced Clarke to turn himself in, Kells will give the unique Exemplar's T-60 Torso.