There are a number of detective-style quests in Fallout 4. Human Error is one of the more complex ones. First, find the walled community known as Covenant in the northern section of The Commonwealth. Speak to the doorman, Swanson, and take the SAFE test to gain access to the community.
Once inside, look for and speak with Honest Dan, an unfriendly guy who could be mistaken for a Raider. You'll learn about a missing caravan. Talk to the other villagers to learn more about it. Leave the village and follow the quest waypoint indicator to the caravan's remains. Look for a cooler and open it to find Deezer's Lemonade.
Go back to Covenant and talk with all the villagers until you've exhausted all conversation topics. Take note of Deezer and talk to him until he offers you lemonade. Be sure to talk to Honest Dan last.
Note the locked house in the village. Pick the lock or steal the Covenant House Keys near Penny in Doctor Patricia's office. Search the house for another set of keys and a note that has Jacob's password. Enter the office building within Covenant and access the terminal.
After reading the information in the terminal, leave the compound and follow the waypoint west to a sewer pipe near a lake. Enter the sewer to access a compound. Explore the compound until you meet Doctor Roslyn Chambers.
The resulting discussion with the doctor will present a number of choices:
Reject the doctor's offer, kill her, use the terminal to free Amelia and speak to Honest Dan for the reward.
Reject the doctor's offer, kill her, use the terminal to free Amelia and travel to Bunker Hill to get a reward from Old Man Stockton.
Accept her offer, let her deal with Amelia and accept the doctor's reward.
The quest will conclude after you've made your decision.