A Protective Covenant For Clues In Queens
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Notes. The note alludes to the shrine password used during Visions in the Fog – the password, "MoThEr," is written on the side of a locker next to a poster of the periodic table, which arranges all chemical elements.
IIRC the easiest way to do the quest is just to sneak into the house immediately to your left as you enter, steal the computer password from the end table left of the door, then go to the house at the end of the settlement, where you see the jail cells, and use the password on the computer.
If you destroy the institute, the covenant quest chain no longer starts. You need to acquire the settlement earlier in the game.
To find Jacob's password to unlock the terminal in the Med-Tek facility, you must first hire MacCready as a companion. To do so, venture to The Third Rail, a bar in the Goodneighbor settlement. Hiring him as a companion costs 250 caps, but this can be reduced with a successful Charisma check.
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.
The bunker is locked with an inaccessible terminal until the password is obtained during the Brotherhood of Steel quest The Lost Patrol.
Inside Covenant, players can find a few things that raise suspicions, like an abandoned bed roll, a note that talks about the rules of Covenant and how not to talk about Synths, and self-help books. Yet, none of this leads to concrete evidence of the fate of the caravan's survivors, or Covenant's involvement.
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.
The Institute may do wrong, but they have the resources to literally rebuild what was lost in much less time than any other existing faction. If you destroy that, you could set back humanity's progress by a huge amount, if not destroy it's chances of ever recovering from the Great War.
If you are not worried about role-playing just let Amelia die. There are no repercussions for doing this and it keeps the settlement friendly.
