At the quest For the republic II, you need to find the bunker of the BoS, and elimante it (if I remember right) but for some reason, after I found it, nothing happens, then I get taken to their bunker, I help the BoS, steel it says "Find the hidden bunker of the BoS" , then I do like I was toll'd, elimanate them, I did, still nothing happens! This is very anoying, seeing that it doesnt allow me to continu story line the way I want it (yes, can still help yes man, but I dont want to do it that way).

Any one know's why?

So you killed them all? You killed every single member of the Brotherhood of Steel in that bunker and you returned the Quest completed to Colonel Moore?

I killed all, that was the thing that was toll'd to do, but it didnt complete, neither did I get any quest update when I found their secret bunker.

Loot the keys off McNamara, Hardin and Taggert. Use them on the terminal in the room Taggert was in, generate a password, use the other terminal to destroy the bunker, quest complete. No need to kill all of them with your weapons when you can blow up their reactor.

note: the reactor won't blow (and you won't get a quest update) until you leave the bunker back into the wasteland.