In a position like the NSC, the officer in question is expected to follow the chain of command, but has access to the whistle blower route if the answer provided by the chain of command does not effectively respond to the complaint. By that, it means that the answer returned back down the chain does not clearly identify a reason that obviates the complainant’s rationale for complaining.
That’s this former O-3’s take.
For waste fraud and abuse, violation of safety regulations, etc. Not because you don’t like your bosses boss and no one will “fix” it for you.