Old Man Stockton of Bunker Hill has recently lost a caravan near Covenant, led by his daughter, Amelia. Understandably worried, he hired an investigator by the name of Honest Dan to figure out just what happened to her and his caravan. Trouble is, the obvious first step in the investigation turned out to be a dead end, thanks to the unhelpful nature of Covenant's residents.
The first stop can be at the wreckage of the Caravan to the northeast. Search the cooler or the ground to find Deezer's lemonade.
The primary option is, however, finding clues in the Covenant compound:
Penny Fitzgerald and can be baited into implying that Covenant's involved in the attack, with Persuasion. She will mention a Compound.
Talia McGovern can be scared into mentioning the Compound by asking about synths, then implicating Honest Dan as a synth.
Jacob Orden's terminal is another source of clues. It's Master locked, requiring proper perks or filching Jacob's password paper from his home by the entrance (with Advanced locks).
Once at least one clue indicating the existence of the Compound is collected, the assignment shifts to finding the secret Compound. Orden's terminal pegs the location down at the Mystic Pines, near the pond. It can also be located simply by exploration.
Honest Dan can be informed of the Compound once it's located and he will meet the player there. At any rate, Jacob Orden will accost the player by the exit and offer a 100 caps bribe to stop the investigation (doesn't affect the quest). Alternatively, a hard Persuasion check will result in him sending word to the compound, allowing for negotiations.
The Compound is located on the other side of the lake, in the central of the three drainage pipes.
Inside, Manny accosts the player at the entrance. Beyond simply gunning him and everyone down, the player can try to persuade their way through by stating they want to negotiate, investigating the lost caravans, or threatening his security team into submission (respectively medium, hard, and very hard checks).
Follow him deep into the compound to find Doctor Roslyn Chambers (assuming violence doesn't erupt). Chambers will explain her motivations and offer a deal: Match the contract price and kill Amelia. Honest Dan will naturally reject this notion.
At this juncture, there are three possible options: Accepting the deal (and killing Dan, if he tagged along) or rejecting it to save Amelia (necessitating a total wipeout of the Compound).
To rescue Amelia, use the terminal by the bed on the lower level, then talk to Dan to receive the reward (300 caps, more with a Persuasion check).
Search Covenant for Clues
(Optional) Search destroyed caravan for clues
Find the location of the secret Compound
(Optional) Ask Dan about Synths
(Optional) Talk with Honest Dan
Find the Covenant Compound
I tried to convince Jacob Orden to give me the Stockton caravan survivors peacefully. He said he couldn't make that deal, but he'd send word ahead to the Compound so I can make my case to them.
Search for any caravan survivors
Find Old Man Stockton
Conflict with the armed guards at the Compound was inevitable. Now I have to fight my way through them to find any survivors of Stockton's caravan. Especially Amelia Stockton.