Well I'm at it again, with my creative juices on my Cybertronic story running low I've been thinking about writing some stories about my two other armies Bauhaus and Capitol. my first idea was based on some research into US involvement in Latin American countries, with my Bauhaus army fighting the spread of a dangerous mutagenic drug called "Deasin" and trying to rescue an archeological expedition that is being held by a drug cartel. then I thought about more modern drug wars, and I thought about making the story about my Capitol army instead and giving it a more modern spin with the drug being synthetic. either way the archeological team that the army is trying to rescue has uncovered something very big about the past of the solar system, as well as who it was that originally sealed the dark legion on Nero. I'm not going to say much more, but I will say that it's very Mass Effect.
so my question is: which version of the story should I write? should it be an 80s drug war with Bauhaus, or a 2000s drug war with Capitol?

Both sound like good ideas. You might want to look at the old Venusian Crusade campaign for MC RPG 2nd edition. It had a part about who sealed the dark legion out I think in it.

roll up the army commander using the rpg rules and then ask yourself where is this guy who would follow his command?

I agree with Dungen. Roll his history with the RPG system. Great way to give fluf to your army. Then again, I come from an RPG background so I'm always looking for a story to tell

also note that the "previous life table" in the cybertronic sourcebook is very useful.