Human Error

Human Error is a quest in Fallout 4.

Detailed walkthrough
The Sole Survivor might hear about Covenant from settlers 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 could 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.

Contrary to other settlements around the wasteland, Covenant is surrounded by tall concrete walls peppered with defensive turrets, and the houses and the yard are in oddly pristine condition. The Sole Survivor even mentions how everything looks almost pre-war. Speak to Honest Dan. He'll explain he has been hired to investigate a missing caravan and find Amelia, the missing daughter of the prominent Stockton family. He also suggests the inhabitants of Covenant might be involved in both cases. He also offers to split the reward in exchange for help in the investigation. Passing speech checks with him might net more caps and info.

Exit Covenant and head north-east along the road to find the remains of the missing caravan and recover Deezer's Lemonade but little else. Questioning the inhabitants of Covenant yields little info, 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 side of the settlement to discover a holding cell, a bookcase with self-help material and a locked computer. Hack the computer when no one is looking to find out Covenant's real purpose. 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 Ogden or pick the lock to the house directly left of the gate and find the piece of paper near the door. You can also find the location of the Compound at the office terminal. The door and the computer are bother Master locks.

Once learning about the existence of the Compound, one option is either talk to Dan or go alone. Trying to exit Covenant, Jacob 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.

To find the Compound, head to the fishing spot west of Covenant on the other side of the lake and enter the outflow pipe. If the Sole Survivor told Honest Dan about the Compound, he will be waiting inside and will follow. Continue along the pipe to face armed guards and turrets. By successfully passing a speech check, the Sole Survivor is escorted deep inside the complex to meet Doctor Chambers. Otherwise, fighting through the complex becomes necessary. On the way there clues about people being held captive and ongoing experiments/torture can be found.

Once confronted by the Doctor, she explains 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. Improving the test involves establishing a "baseline" and then requires various forms of psychological and physical torture to incite reactions from the subject. She also explains, the reason for capturing Amelia is because they believe she is a synth infiltrator.

At this point, The Sole Survivor has two choices.
 * 1) Deciding to side with the Doctor, Honest Dan will become hostile and killing him will be necessary. Also, inspecting Amelia's body reveals she was indeed a synth. Return to Jacob to win Covenant as a usable settlement.
 * 2) Deciding to side with Honest Dan and free Amelia will turn the Doctor and the rest of the Compound 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 computer terminal. Speak to Dan to receive a reward. By passing increasingly harder speech checks, more reward can be earned. Choosing this option will also turn the inhabitants of Covenant hostile. Kill them all except Deezer to win it as a usable settlement.

Bugs

 * Deezer's Lemonade, might not spawn, if it does it cannot be acquired.
 * Honest Dan becomes hostile upon entering Compound
 * Dr. Chambers' dialogue won't start if Honest Dan is already dead
 * The gate leading into the covenant might already be open even if it's the first time visiting the place, and all the characters act like having already been there and Honest Dan is nowhere to be found, making the quest impossible to complete or even start.
 * After finishing the quest Swanson can't be killed.
 * Wearing a Power Armor helmet with the Targeting mod makes Dan hostile when you enter the sewer, and the rest of the NPCs inside the Compound. Need to unequip the helmet before going in.
 * After freeing Amelia, the doctor wont turn hostile and will hang around saying "All I did was for the greater good!"