Human Error

Human Error is a side quest in Fallout 4.

Detailed walkthrough
The Sole Survivor might hear about Covenant from settlers, Diamond City guards, or a passing trader, which will put its marker on the map and a quest entry to "Investigate Covenant." Upon approaching the gate, the Sole Survivor is greeted by Swanson. He explains that to enter Covenant, visitors have to pass a test to filter out "undesirables." By pressuring for information and successfully passing increasingly difficult speech checks, details about synths and the Institute can be learned. Swanson will be adamant about administering the SAFE test to make sure the Sole Survivor is not a synth. After taking a seat at the table and answering all the questions, the gate to the settlement will open up. It is impossible for the player character to fail the test.

Unlike other settlements around the Commonwealth, Covenant is surrounded by tall concrete walls sprinkled with defensive turrets, and the houses and the yard are in pristine condition. The Sole Survivor even mentions how everything looks almost pre-War. Several companions will voice suspicions that the village is hiding something, although none of them seem aware of its true nature. Speak to Honest Dan. He will explain he has been hired to investigate a missing caravan and find Amelia Stockton, the missing daughter of the prominent Stockton family. He also suggests the inhabitants of Covenant might be involved in both cases. He offers to split the reward in exchange for help in the investigation. After the player character agrees to help, Dan will provide what he knows in the form of a note, Caravan Details. Passing speech checks with him may net more caps and info.

Exit Covenant and head northeast along the road, then go east at the junction to find the bodies of Fred O'Connell, his guards, and the remains of the missing caravan. A can of Deezer's lemonade establishes that the caravan had visited Covenant (if the quest has not begun, the cooler box will not be accessible yet). With a Perception of 6 or higher, a blood trail on the road close to the scene can be investigated to reveal that "the blood trail leads roughly in the direction of Covenant." Questioning the inhabitants of Covenant yields little info as they are adamant about having nothing to do with it. They are also oddly nice, almost saccharine.

To find more clues, enter the house on the far end of the settlement to discover a holding cell, a bookcase with self-help material, a locked terminal, and a non-functional radio. With Luck of at least 9, the player character can "fiddle" with the radio and briefly pick up a voice broadcast referencing the remains of Stockton's caravan. Outside one of the houses is a bedroll left by the caravan staff, which can be investigated, but it isn't clear enough who it belonged to.

Hack the terminal when no one is looking to find out Covenant's real purpose. Hacking the terminal when not sneaking will turn the whole town hostile. It is also possible to gather information by speaking to one of the settlers, Talia McGovern, and convincing her that Honest Dan is a synth after passing a few Charisma checks. Alternatively, enter the shop and take the piece of paper from the trash can or pass increasingly harder speech checks with Penny Fitzgerald to reveal the clues. Another alternative is to either pickpocket the key from Jacob Orden (the most optimal way is to steal this from him while he is asleep in the guest house) or pick the lock to the residents' house directly left of the gate and find the piece of paper near the door. If pickpocket is too risky, between the hours of 7 a.m. and 8 a.m. the doors to the first house on the left when entering Covenant will be open (in general, all of the buildings in Covenant can eventually be entered without the need to pick a lock, through the expedient of following the residents around until they open the doors on their daily schedule). On the table is a key and a paper that has Jacob's password. Residents may become hostile if they see stealing. They will issue warnings if they see the player character enter the residents' house. One can also find the location of the compound at the office terminal (the door and the terminal are both Master locks) or by obtaining the map to the Compound. Alternatively it is possible to go directly to the Compound without obtaining clues, if the player (not the player character) already knows its location.

Once learning about the existence of the compound, the Sole Survivor can either talk to Dan or go alone. When they try to exit Covenant, Jacob Orden will be at the gate and will try to convince the Sole Survivor to drop the case, even going as far as offering a bribe. If they succeed at a speech check seeking "compromise", Jacob will send word ahead to the compound, and the player character will be able to attempt to negotiate with Manny more easily once inside the compound.

To find the compound, head to the fishing spot east and below of Mystic Pines - an inlet with three outflow pipes, directly west of Covenant on the exact opposite side of the lake - and enter the middle outflow pipe (expect some rad exposure when entering and leaving). If the Sole Survivor told Honest Dan about the compound, he will be waiting inside and will follow. Continue along the pipe to face Manny, armed guards and a turret. Successfully passing a speech check with Manny will allow the Sole Survivor to be escorted deep inside the complex to meet Dr. Chambers. This check is easier if Orden sent word ahead about a compromise. Honest Dan has unique dialogue if he is also being escorted. Otherwise, fighting through the complex becomes necessary. On the way there, clues about people being held captive and ongoing experiments/torture can be found, whether fighting or being escorted.

Once in the presence of the doctor, she explains her motivations, and her intentions of trying to reveal hidden synths who infiltrated the populace by creating and perfecting the SAFE test, a sort of psychological test involving studying reactions of the subject to several situational questions. It can be learned that as a child she was affected by the Broken Mask incident, or a similar incident, losing both parents. Improving the SAFE test involves establishing a "baseline" and then requires various forms of psychological and physical torture to incite reactions from the subject to validate the results. Dr. Chambers may also explain that the reason for refusing to release Amelia is, that she is most likely a synth infiltrator - hence why her caravan was attacked to seize her - but that even if she is not, releasing her now would compromise the operation at the Compound. Dr. Chambers will offer to pay the same caps reward offered by Honest Dan, to be allowed to dispose of Amelia Stockton. Accepting her offer will result in the promised caps reward, freedom to come and go in the Compound, and (after speaking to Jacob Orden) obtaining Covenant as a settlement.

An alternative path to reach this quest stage is to bypass both Dan and Covenant entirely, and simply proceed into the compound. Then one has to either pass the hard speech check with Manny or fight off all residents except for Dr. Chambers, who will remain non-hostile. Talking with her will then start the quest. Another option is to ignore the doctor altogether and moving up to Amelia's prison cell to speak with her, which will also start the quest. Yet another way to start the quest is to peacefully gain entrance to Covenant, then gaining access to Jacob's terminal unseen (e.g. without the inhabitants becoming hostile), which will trigger his dialogue with him upon attempting to leave the settlement. One can then move to and enter the compound through the sewage pipe, initiating the quest.

At the point of reaching Dr. Chambers and Amelia, the Sole Survivor has several choices:
 * 1) Deciding to side with the doctor. If accompanied by Honest Dan, this will cause him to become hostile, and killing him will be necessary. It is not possible to kill Dan earlier as he is marked essential until the final part of the dialogue is completed. Amelia will be killed by the doctor if she is not killed by the player character. Inspecting Amelia's body after death reveals that she was indeed a synth. Return to Jacob to win Covenant as a usable settlement. There is also a reward of 300 caps from Dr. Chambers at the completion of this quest.
 * 2) Deciding to side with Honest Dan and free Amelia will turn the doctor, Manny (who may be present) and the rest of the compound (apart from the heavy machinegun turret at the entrance) hostile, making it necessary to kill them all. Amelia is in one of the cells up the stairs which can be opened by using the terminal or by picking the lock. Afterward, speak to Dan to receive a reward. By passing increasingly harder speech checks, more rewards can be earned. Choosing this option will also turn all inhabitants of Covenant hostile, except for Deezer and Dora (the cat). Kill all hostiles to win Covenant as a usable (albeit with some difficulties) settlement.
 * 3) A third option will make itself available if the Sole Survivor does not bring Honest Dan to the compound. After freeing Amelia, as they would when siding with Dan, they can turn the quest in to Old Man Stockton, who can be found at Bunker Hill. He will give the same 300 bottlecap reward offered by the doctor and Honest Dan, although there is no way to increase the reward through speech checks. If the player character has already completed Boston After Dark, the Sole Survivor can remark about making a habit out of helping him. The quest cannot be turned in to him if Honest Dan accompanies the player character, however; he will simply say that he already contracted someone to find the missing caravan. Upon returning to Covenant, all inhabitants will be hostile, and it will be necessary to kill them all except Deezer to receive Covenant as a settlement. If choosing this option, almost everything inside the compound will be considered stolen, making it very complicated to use this settlement. Old Man Stockton is a nonessential character and can be killed. If he has already been killed and the Sole Survivor chooses to save Amelia, without bringing Dan to the compound, the quest will say "Failed" immediately after the "Find Old Man Stockton" objective appears and it becomes impossible to complete.
 * 4) A "fourth" option is also available to the player character. If they arrive at the compound without Honest Dan, they can engage Amelia in conversation before freeing her or letting her be killed by the doctor and she will direct the player character to Old Man Stockton, claiming he will give a reward for freeing her. The quest will update as though the player character has freed Amelia and the quest marker will lead them to Old Man Stockton. If the player character leaves Amelia in her cell and turns in the quest to Old Man Stockton, the quest will be complete, only in this case, upon return to Covenant, all inhabitants will be friendly to the player character. If the player character has passed the speech check at the compound, all inhabitants there will remain friendly as well. Although everyone is still alive, this option offers the least amount of rewards, as there is no way to obtain Covenant as a settlement.
 * 5) Releasing Amelia after agreeing to do the deal with Dr. Chambers causes the Compound to go hostile, and Covenant does not ally freely as a settlement.

Bugs

 * If entering Covenant late in the game after one has destroyed the Railroad or sided with the Institute, the residents of will immediately be hostile - but not until after taking and passing the S.A.F.E. test and walking through the gate. If Curie is a companion in this situation, she will also become hostile.
 * The gate leading into Covenant might already be open upon first visiting the place, and all the characters act like the Survivor has already been there and Honest Dan might nowhere to be found, making the quest impossible to complete or even start. This may be caused by completing the main storyline before obtaining the quest.
 * One fix is to kill all residents, thus gaining access to the workbench, then resurrecting residents in order to gain the settlement if the quest cannot be started.
 * Another option is to resolve the quest via console commands, by first resetting the quest with, then talking to the Jacob Orden, and using the console with , and talking to Jacob again. This will complete the quest as if having sided with Covenant and unlocks the town as a settlement.
 * At the caravan, for the optional objective, Deezer's Lemonade might not spawn or be interacted with, making it impossible to obtain it.
 * This can be fixed by manually progressing the quest via the console command . Alternatively, both the Lemonade and the cooler can be activated with the and  commands. Another option is to simply reset the quest via.
 * Another workaround is to pick up "Deezer's Lemonade" by commanding a companion to check the cooler, trade with the companion and one will find the lemonade in the Aid category.
 * Alternatively, if the above companion workaround does not work, but the lemonade can be grabed, one may drag it to the nearby Taffington Boathouse, drop it, go into crafting mode, and store the item in the workshop. This allows for manual retrieval of the item and will progress the quest.
 * Penny Fitzgerald may not talk to the player, only saying "enjoy your stay" when interacted with. Sleeping seems to fix the issue.
 * When stealing Jacob's password, Covenant house key, Covenant office key, or SAFE report, it is possible the entire town will turn hostile regardless of whether being detected or not.
 * Dr. Chambers' dialogue will not start if Honest Dan is already dead.
 * After talking to Dr. Chambers and agreeing with her, one can quickly run up to Amelia and tell her everything will be okay. By doing this one can complete both the main quest and also the optional quest to free her.
 * After freeing Amelia, the doctor will not turn hostile and will hang around saying "I will not beg for my life," and "All I did was for the greater good!"
 * At the end of the quest, when talking to Honest Dan, if the conversation is interrupted just after getting the reward by walking away, the player can talk to him and claim the reward again. This can be repeated indefinitely. Note that the Charisma checks for more money are not reset.
 * After finishing the quest, Swanson cannot be killed unless he is within the borders of the settlement. Since he will rush out to attack the Sole Survivor, it may be necessary to kite him back to the gates.
 * If clearing out the compound before finding any clues leading to it or its existence, and freeing Amelia, Honest Dan will not spawn at Covenant, and the quest will stay bugged and impossible to complete. The Sole Survivor may get stuck at "Look for caravan survivors" even after freeing Amelia.
 * Wearing a power armor helmet with the targeting HUD mod or using Berry mentats turns Dan hostile, as well as any other non-player characters inside the compound. To avoid this, simply unequip the helmet. Note that this bug also applies to companions wearing a modified power armor helmet.
 * Wearing power armor with the Tesla coils torso mod inside of or around the entrance to Covenant may turn nearby inhabitants hostile. The solution is to exit the power armor before entering.