I've looked through the fourms and I couldn't find anything relating to what is happening to me.

I didn't have any issues with completing the Khans sections, I killed Papa Khan and got them to make a truce with the NCR, but when I got to the part where I must destroy the Brotherhood of Steel I reached a problem. I have already have meet the Brotherhood and have become a member of them, and I get no dialoge option reflecting this. Also when I suggest a non-violence path, she tells me that she won't allow it, and that I got lucky with the truce with the Great Khans. Anyone got any ideas on what to do.

Go inside the bunker to the virtual reality simulation room.

Use the computer console on the wall and select "Generate Self-Destruct Password" and go from there.

Though I thought you could have a truce with NCR if you keept McNeerma(sp) as Elder?

If you made Hardin the leader of BoS, you have to wipe them out.

If you made McNamara the leader, you can make a truce between BoS and NCR

I'm in the same spot. I'm waiting for a patch/mod that allows a truce with the new elder.

Or, if you kept the current elder in position, talking to him should open the truce option.

Well crap, I think I figured it out, I made Hardin the Elder. Looks like I got to kill the brotherhood to finish the quest, thanks for the help.

Yeah, there are some hints that Hardin is only interested in expansion of the violent kind, but not enough hints for a player to make a definite determination. So, the quest isn't really broken, its just that the quest leading up to it isn't clear.

I kind of surmised that Hardin would be a bad Elder. Ramos says as much and the In The Dark quest lends credence to Elder McNamara's concerns. Also, trying to find a way to oust the Elder seemed sketchy. At the same time, none of those facts come out and tell you that Hardin isn't a peaceful person. You don't really find that out until he requests that you exterminate the Van Graffs. Not because they are evil, but because they have a huge cache of Energy Weapons.