Has anyone of you considered such a scenario? It's by far one of my favourite drama scenarios when a captain/admiral has to go against their own chain of command. TV series, books, you name it.
Consider the Earth Alliance Civil War in Babylon 5 when Sheridan was forced to fight his own government after the latter gradually became a dictatorship.
Could something like that happen to Honor and the Star Empire of Manticore? A Janacek type usurping power, but actually being competent

in doing it, fabricating whatever "truths" he needs to sway public opinion, cornering political rivals until they stay silent or outright join him, etc. Imagine Honor on a long deployment (long term goodwill mission in the League, whatever), our Big Bad Guy does his thing at home and takes over... Honor and her fleet are left the only "free" part of Manticore and out of nowhere Honor receives a recall order from the Admiralty, some outrageous orders (stand down? demotion?) and finally she is forced to fight her own people. Would she? Would they?
Far fetched? Probably. The Empress would stop it? Possibly. We have seen the sovereign has limits on his power (was it King Edward in A Call to Duty that said something along those lines to his son? Even the King has limits to his power when it comes to political struggles with parliament?), so yes, it's a highly unlikely train of thought, but what if...