When Scenario Five is ordered on Tau Volantis, the Admiral speaks about how "the separatists" will probably create an Earth Government in the vacuum left by the Sovereign Colonies. What does this implication mean for the idea that EarthGov is the SCAF's enemy? Caiden says: "We realize that this will effectively negate our ability to fight the way against the separatists. They will no doubt take power and form an Earth government in the vacuum we leave behind..."
So does that mean the Sovereign Colonies were NOT the separatists? I assumed the SC were, you know, colonies fighting for their independence... But this makes it sound like the SC is the in-place government and that the separatists are what will become EarthGov... But then why would they be called the Soveregin Colonies??
I'm confused. I've read both books and scoured the games, but still confused as to this point. (I'm writing an adaptation that follows the events on Tau Volantis, and this is one of the only parts I'm stuck figuring out..)
Earth and its colonies were all under the control of EarthGov in the late 2200s. However, the official NAME of that government was not yet called "EarthGov," but rather something else.
As the outer colonies got tired of the government's meddling, they wanted their independence. Thus declaring themselves the Sovereign Colonies, they broke away from Earth's colonies, marking the beginning of the Secession Wars.
When the Secession Wars ended in 2314 with the Sovereign Colonies' defeat, Earth's government regained control over its colonies, but maybe they decided it was time to take a different approach and a different ruling method. Thus the government decided to change its name so as to imply to the people that this is a new order, and THAT was where "EarthGov" (in name) finally came into existence.
There's been a HUGE retconn with DS3, from what I gather from a convo at reddit it is possible that there was a previous earth gov of sorts that created the colonies in the first place, or maybe those colonies were the result of individual countries or even organizations. Point is earth was going down at the time (maybe due to the resource wars?) so the colonies organized their own government with the SC and allegedly took over earth. The secession war seems to be between a group on earth that wants to be in charge of everything or simply isn't cool with how SC is doing things since there seems to be a lot of earth people involved in SC (the private in tau volantis you play as at the beginning of DS3 is from earth and so is his entire family as mahad says) so the secession war simply shifted power over human space from the colonies and back to earth. SCAF destroying their ships is very similar to what the german empire did at the end of WWI to prevent those from going to their enemies as reparations
I think there is alot of good stuff here, the way I see it:
SCAF = Government before EarthGov, practically controlles everything but a group of colonies seeds from the Colonies (the successionists) and effectively causes a civil war.
The war rages on for a undetermined amount of time and SCAF start to lose, they have access to the black marker and other marker sites (when you turn the power on the Roanoke you can see the presentation Serano gives to Mahad about the marker sites in the briefing room).
Using this access they triangulate the signal that is 'powering' the markers  so they go there (Tau Volantis), it doesn't work out so they scrub the mission (Scenario 5) and the other marker sites and bury the information so that the successionists don't find it .
Obviously this fails as Dead Space happens (and Dead Space Martyr before ).
And finally, at some point after all this they scuttle their fleet and are cosigned to history.