So im on the For the Republic Part II mission where im supposed to find and deal with the BoS and ive found them and done all the missions for them but that For the Republic Part II quest still shows incomplete, why is that? do i have to kill the BoS to progress?

That would be what she tells you to do.

so my only option is to kill them? thats rather lame how do i get power armor training if i kill them? also there are like 3 options on every other quest why not this one : (

I didn't say that was your only option. I said that's what she told you to do.

Since someone else will tell you anyway, I guess I'll ruin the fun of figuring it out yourself. You need to keep McNamara as the head. If you try replacing him, it's a no go. You'll have to kill them.

i did keep him and he said he doesnt think the NCR are a threat anymore but the mission still says to deal with them

and i tried going back to hoover dam and talk to the lady there but it didnt work either

You have to ally them to get it to work. And you have to do both questlines.

oh ok that makes sense but what do you mean both quest lines?

ok nevermind i got it