The Enclave in Fallout 3 seemed like a big frigging mess of confusion. I was scratching my head a bit when I saw sentry bots mowing down tesla armor clad troops
I'll let Andronicus explain, if he wants too.
Oh boy.
I'll take a crack at it though. Truth be told, I'm not really sure what happened myself. *cough* bad writing *cough* wanting to somehow get the player involved in a
moral! decision *cough* trying to make Raven Rock more interesting by shootin stuff up *cough*
Lore-wise, though (and leaving Bethesda out of this) we can assume a few things when breaking down what I like to refer to as the "Raven Rock Incident".
1. We must, for all intents and purposes (and though I didn't believe this initally) take what happened at the RR to be a "rebellion" against the legitimate President of the United States, John Henry Eden. Thus we see Eden's actions against those Enclave troopers who (for whatever reason) countermanded the President's orders, as "putting down" a insurrection. Those troopers who were killed were, in my mind, guilty of high treason (even if perhaps, they didn't fully know it).
2. With this in mind though, what must be understood is that Autumn still
believes that he is being a loyal servant of Eden, even after he as obsconded with a portion of the Enclave forces and publicly countermanded a direct order from the President. When he is at project purity, he makes the statement that he cannot bring himself to "abandon" Eden because the "chain of command must be upheld" (direct quote). If Autumn still thought he was being loyal, then its likely that a large portion if not all of "his" soldiers, thought that they were as well, and thus terming it a "rebellion" may not be the best terminology.
3. What we now have is basically two factions within the Enclave, "Edenists" or those loyal to President Eden (whom I believe to have made up most or a large portion of Raven Rock's personel and thus AAFB's) and the "Autumnists", or those who followed the mad Colonel Autumn and who were being mowed down by Eden's private peacekeeping army and who stood ground at the purifier.
4. The reasons for Autumn's countermanding of orders and his flight out of Raven Rock, are preminently due to the disagreement between he and President Eden over how best to handle the problem of the wastes, Autumn wanted to use the purifier (which is why he tried to defend it) and Eden simply wanted to use the GECK powered purifer to amplify and distribute a lethal virus ala' President Richardson (which, for the Enclave, is really the best option, as when you insert the virus the end slides say the Enclave "wins", that only the Enclave are allowed to thrive.)
What is the Raven Rock Incident then? The answer is: there is no clear answer. Its not quite a full rebellion, as we can see that the "rebel" leader was still loyal to the President, but clearly its not just a domestic dispute or a "poltical party" disagreement (unless the Enclave settle such matters with lasers).
I know I'm not much help, but like I said, I'm not even fully sure what happened.