So i am trying to destroy the master. I read about a diplomatic way in which once you barter for the COC card, and you have some robes on, you are able to work your way up the stairs to talk to Morpheus, and you can get him to take you to the master. I have Vree's autopsy report, and i want to convince The master to commit suicide. Now i have the robes, and in the walkthroughs i have seen, people are able to climb up the stairs peacefully and then talk to Morpheus. Now here is the part i am having trouble with. When i get to the level before, and the level where Morpheus is at, i am immediately attacked. I do have companions. In the walkthroughs i have seen, they do not have companions. So are my companions holding me up, or am i doing something wrong?

I know the guys that accompany you from the Followers of the Apocalypse will cause you to be attacked. Normal companions might as well, but I'm not sure - never gone there with any.

You can try sneaking using stealth boy. Or you can use the infinite turns bug.

you must leave your companions behind....also if he have your fateful dog..well kill him or you get trouble.
no weapon, wear your robe.
this way you can earn some experience with talking to people....or you can just forget all take your companions
and weapons and kill the scum (hey nobody will survive the explosion anyway).

Yes, unfortunately you can't have any companions with you. I had to shoot my faithful Dogmeat just outside the cathedral, as he was too loyal and could not be reasoned with.

There's a mod to fix this problem. If you're interested -> http://falloutmods.wikia.com/wiki/Fallout_NPC_Mod.

Thanks, I didn't know there is one. Although this was the only time I needed to do this, and as the game is pretty much over, I might just shoot him next time too. ;)