There's certainly some "interference" between the Council and Alliance chain of commands. As I understand it, Shepard ceased to be an Alliance soldier when he was deemed KIA in 2183 after the Collector attack on the Normandy SR-1. Of course, if he was deemed MIA then it's a different story altogether.
It is illogical that a Spectre would still be subjected to their former chain of command. The Council and the Alliance won't always agree on all subjects, and Shepard would be bound to follow orders from both organisations. The moment they disagree you get a conflict of interests where the Council would naturally overrule the Alliance.
e.g.:
"Commander Shepard, the Council believes you did the right thing. Keep up the good work!"
"Commander Shepard, the Alliance believes you committed galactic genocide. You are to be summarily executed, right... now!"Get the idea? As a Spectre, Shepard MUST put the good of the galaxy BEFORE the interests of the Alliance, or even the Council for that matter. But, hey, I still welcome the opportunity to laugh at the crowds as they try to ridicule me for believing on a "fictional" Reaper invasion!
"Ah, yes, Reapers...
Modifié par OdanUrr, 16 juin 2011 - 07:01 .