Possible *SPOILERS*

Ok, so I just started the quest line of "Still in the Dark" where I discover the Hidden Valley bunker that the Brotherhood has. They put an explosive collar around my neck and told me to go get rid of the NCR trooper that's in a separate bunker. I told the NCR guy to leave, than when I go back to the hidden valley bunker and use the intercom the door opens up and nothing happens. When I go in and get inside the next door, Elder McNamara is waiting for me at the bottom of the stairs with 3 other guards and tries to kill me. I think they should be friendly, but all they do is try to attack me when I enter. I can't leave the area cause I have an explosive collar around my neck and I can't go inside or i'll get [censored]... I don't know what to do.

I've tried killing the ranger and telling him to leave, I've even tried waiting a few days outside of the hidden bunker than going inside. They're just red on my radar and always ready to kill me. The only save I have is right before I enter the rangers bunker, so i've already got the collar on... I don't know if there's a way to raise my rep with the Brotherhood in console so they won't try to attack me or something.. I also don't have any NCR or faction armor on.

I think I may be able to reset the quest, but I don't know what the quest id for "Still in the Dark" is, does anyone know?

did you tell him to leave because the BoS is near? if so they will attack you for that.
edit:..i just realized what i said makes no sense but hey at least im helping you get some attention on the topic lol

I've tried just killing him, but they're still hostile when I go over to the bunker.

yea than its a gltich.. to bad man

I had the same thing happen once, then I realized my mistake.

If you are wearing NCR armor the brotherhood will attack-on-sight.

Otherwise if you gave away the Brotherhood base in your dialogue with the NCR ranger you made the entire Brotherhood hostile. Unlike in previous games the brotherhood are NOT the "good guys" of New Vegas.

I've tried going in there and just killing him, but when I go back to the brotherhood bunker, they're no one in the first section and when I go through the second door they're just waiting at the bottom of the stairs to kill me. I'd like to just reset the quest, but I don't know what the quest id is..

I'm not sure if just assaulting him triggers BoS hostility. It may because you're drawing NCR attention to the area. I used the speech check option and was fine.

I killed him and I got congratulated for it because I displayed combat prowess.

I got called a brute when I killed the ranger =P.