Is it better to kill or disable mr. House before I go to his hidden bunker and before I do the quest "render unto caesar. I want whats in the bunker and the dogs brain but also want to stay on the good side of the ncr at hoover dam
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Okay, I don't really know what you're asking.....
If you simply disable Mr. House, then he will be put back into the chamber, and slowly die from infections and/or diseases, so if want to be kind, kill him.
In the Bunker under the Fort is very very little. Nothing of interest, just a load of standard scavenge items.
If you mean the brain of the dog in the fort, doing so will cause the entire Fort to turn on you, so I would advise against it.
None of these make the NCR hate you.
It will have no effect either way. The only thing that I noticed is that he gives you a little speech before you go in if he is still alive/connected. It's just a blank screen if you killed/disabled him. The legion will not know what you do down there no matter what you do. As for the dog brain, I think that you can talk the dog trainer into giving it up peacefully.
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