Well, inspired by Acroyear's post I'll put mine up for your ideas and thoughts.
The time: Late 2367
The situation: K'mpec, Chancellor of the Klingon Empire is poisoned and is slowing dying. He appoints Jean-Luc Picard as Arbiter of Succession. Jean-Luc refused to accept Torel Son of Durus's bid to be Chancellor which inevitablly results in the the Klingon Empire falling into a civil war, with forces allying with Gowron or Torel. Lt. Worf resigns his commission and joins the side of Gowron.
The Federation Council deems it's best to lend support to neither said during the Civil War. Unbeknowst to the Council Torel was recieving covert support from Sela, a Romulan operative.
The campaign: Essentally, the episodes will be effected by what the players do. The Federation Council finally agrees to lend aid to Gowrons forces but it is to late to have a major effect. Gowron will be killed, Torel will become Chancellor, Klingons will either remain in the Empire or leave the Empire and join the Federation. The Klingon Empire and Romulan Empire ally and seek to destroy the Klingon traitors, even if that means declairing war on their Federation allies.
The Romulan Empire also forms an alliance with the Cardassian Union, as their first act of support to their new allies they root out and eliminate many of the Bajoran Resistance. Those members of the resistance that manage to escape flee to Federation space and join the Federation/Klingon alliance.
The players will be playing through this, trying to stay alive during the fighting and advance themselves. No matter what they do before the above events it'll be very very hard to prevent them for happening.
Sub-Plots: Give me some ideas to go with the base series story. Fun twists, anything at all.
Ofcourse, I can't think up a good name for this series, so if you have an idea, let me know!
Kyle