Covenant is a potential settlement along the main road west of Taffington House. In order to enter the location, you have to take a test first, tailored closely to the G.O.A.T test given in Fallout 3.
For the first time you visit Covenant, you’ll find the mercenary named Honest Dan. Talk to him to learn about Stockton’s missing caravan. Accept the job to start the quest “Human Error”.
The Covenant House Key is found in the small table in the corner in Penny’s store. You can steal it out in the open as long as you crouch and stay still within range of the key. The cash register should block Penny’s line of sight and wait until the doctor turns around. Use this key to open the first house to the left from the entrance. Here you’ll find a note about a reminder to every resident of the town, Jacob’s terminal password, and another Covenant House key.
To get you started, head to the location of the lost caravan. Loot the bodies and containers and you should find Deezer’s Lemonade.
Return to Covenant and ask around again. With the note you’ve taken earlier in the locked house, you should be able to ask more questions. After that, the house in the middle will be opened when Brian Fritzgerald is inside. You can steal the SAFE test results and Covenant Office Key in the desk in the corner if the coast is clear then use the terminal with the help of Jacob’s password to access the contents. Read the draft to update your objective.
Once done, you have the option to talk to Dan first before heading to the Covenant Compound. As you’re heading out of town, the mayor will attempt to bribe you.
Head to the marked location and enter the sewer from the Water. If you talked to Dan, he’ll be waiting inside. Continue forth and you’ll be confronted by the Compound guards. You can attempt to persuade them but it will require a significant high Charisma level.
After dealing with them, get the Compound Key and enter the first room to the right downstairs. Kill everyone inside and get the Subject 12 Baseline holotape. Continue downstairs then move to the larger area. Head to the left to find a generator with a Fusion Core. Continue upstairs to the north then open the red door ahead. Enter the other door further north to find a jail cell. Pick up the Subject 12 holotape on the table as well.
Continue further west to find the meeting room. There’s another Subject 12 holotape found on the table. Continue forth until you reach the large room with Dr. Chambers. Talk to her to learn more about the synths and SAFE tests. If you have Dan with you, he’ll react to Dr. Chamber’s counter-offer. If you accept Dr. Chambers’ offer, Dan will become hostile and you’ll have to kill him.
After dealing with Dan, Dr. Chambers will kill Amelia by activating the trap in her cell. You can run to the terminal first and unlock the cell first before she kills Amelia. Another option is to reject her offer then unlock the cells to free Amelia. You don’t have to kill Dr. Chambers and Dan gets to live. After this, the mission will be complete.
The room has mattresses, a green steamer trunk, chem station, and armor workbench. You can now leave the area. Take note that if you declined Dr. Chambers' offer and freed Amelia, the residents of Covenant will be permanently hostile towards you and you'll need to kill them all before you can use that location as a settlement.