Since I work for the NCR and the advisor to the Chief says he wants to help NCR rather than Ceasars Legion, how do I kill him off to replace the leader without anyone noticing?

When you are [Hidden] 1 Shot him.

Or "Mr. Sandman" him when he is asleep.

I followed him until he went to sleep.... Once he was in his bed, I assassinated him. To assassinate someone you have to have the Sandman Perk.

Or a powerfist... or just pop a cap and get the hell out of there!

Wait for him to go sit in the outhouse round the back of the building, crouch at the side of it and as soon as hes finished doing whatever it is he's doing and stands up to walk back into the building, bring up VATS and murder him to death with a melee weapon, thats how I did it anyway. Pop a stealthboy, some physco, and read some melee skill mags if you got em.

Did that, worked like a charm .

Groovey :celebration:

You can get the chief to side with NCR without killing him. You have to do stuff for his advisers, then he will be convinced that it is a bad idea to side with the Legion and accept your proposal of helping the NCR.
There is also this Legion rep that is the 1 making the chief want to side with the Legion, if you have high enough speech you can make the Legion rep bad mouth the Khan right infront of the Chief, then the whole lot of them will proceed to shoot him dead.

I shoved a frag mine down his pants while he slept. Nobody seemed to mind.

i walked in there with a couple bars of C4, tossed one on his table, and put the other one on his followers table... walked into a room and KABOOM!! ( i would have totally freaked out if someone threw a a brick of C4 on my desk )

You can also put C4 on his bed and use the detonator to blow it up while you are hidden. Or, for laughs, do the same thing while he's on the outhouse.

I think the best you can get out of Papa is a treaty of non-agression with NCR. I think he won't actually aid them at the dam. His son however will.

Unlike some of the other groups, the Khans "best" ending does not equate their helping you at the dam. If you're trying to be "Good" and get the "best" endings for everyone, consider that assassination might not be a great way to do this.