I have the GoTY version, on PC, and have checked the boxes in the data files (on start-up) to make all the add-ons load.

I have been randomly exploring the Wastelands, and have acquired a lot of Quests by speaking to various characters in the game, and have completed some, but not making it a point to travel from point A to B just to do a quest, so a lot of them are in my Pip-Boy but only approx 14 are completed. I have made a point to not go into any of the areas/quests for the add-ons, as I want to do all the original game first.

I just found Fort Bannister, and killed all the NPC's there, above ground and below. While taking a break from the game I was reading random pages on the FO3 Wiki and found a page for Fort Bannister and it says that with the Broken Steel add-on installed I would have found Aqua-Pura pack Brahmin near the tents, and a Brotherhood Paladin tied up in one of the tents...I saw neither. Is that because I have not finished the Main Story quest line yet?

Have I messed up a quest or time-line by doing something out-of-order, by randomly wandering through the game as I am? I have completed the Main Story quest line up to the point where I've found Dad's holodiscs telling me he's gone off to Vault 112, but I have not gone to Vault 112 yet...so by killing off everyone at Fort Bannister will it have a detrimental affect when I finish the Main Story quest and then start the Broken Steel stuff?

Will the Talon Co. Mercs that populated Fort Bannister respawn?

Thank you for your time and assistance.

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From the Wiki:

"Paladin Jensen and the Brotherhood of Steel assault on Fort Bannister will not appear if the player kills http://fallout.wikia.com/wiki/Jabsco prior to completing the http://fallout.wikia.com/wiki/Take_it_Back%21 quest and beginning the http://fallout.wikia.com/wiki/Broken_Steel content."

Since you mentioned killing everyone above the ground and below, you probably killed Jabsco as well which means that the BoS attack won't be triggered.

Thank you...I must have overlooked that. Have to go back a re-read it more carefully this time.