Star Wars WI: Separatist Alliance ISOT to the Original Trilogy

Turn his back on Old Emperor Palpatine and take his chances staying with the Separatists, yes. Become friends with the Rebels, well...kinda-sorta, best case scenario.

Though they'd likely sign a non-aggression pact and perhaps cooperate on certain occasions, I imagine the relationship would be akin to the American-Soviet dynamic of WW2. They're facing a common enemy; by little means does it make them friends, and one might turn upon the other if/when the Empire has been neutralized.

Rebel leader Mon Mothma & Co., as well as older members of the Alliance, surely remember the reign of terror that Dooku's Confederacy exacted upon the Galaxy mere decades before. And while they may not be as iron-fisted as the Empire that both factions are fighting against, the Separatists are still led by a rather villainous Serennoan Count and a council of evermore greedy, profit-obsessed business tycoons who have presided over and outright engaged in some exceedingly questionable behavior. Google the activities that the Commerce Guilds have been known to perpetrate long before the Clone Wars started, and then you'll know what I mean. The fact that the likes of General Grievous--who'd likely still be asked to hold back on the butchery to avoid alienating the denizens of this time period too much--have been sent along could be a problem. Though, at least retaining its Supreme Commander means that the CIS won't be entirely bereft of a strategically and tactically skilled top military leader.

Long story short, a partnership between the two Alliances would be one of teeth-clenched teamwork and mutual, patently obvious distrust. In my mind, I'm already visualizing a tense and dare I say awkward initial diplomatic meeting between Dooku and Mothma. Yeah, this scenario should be real fun.