Heres an idea I just thought up after reading some of your coments.
The setting.
It is a few years after the Dominion war. The Federation is trying to usher in a new era of peace and deplomacy. However, because of the Federations new policies, some of the more aggresive admirals that rose to power during the war stand to lose a lot. This is beginning to destabalise the political and military leadership and the government is bogged down trying to apease everyone.
Enter Section 31.
Section 31's less than moral decisions during the war has made itself a lot of enemies among the more peacefull factions.
The Federation's new president is planning to shut down S31 for good. However, S31 had seen this coming and refusing to go down easily, using a fleet that had been built during the war for S31's covert missions and teaming up with the more aggresive factions in Starfleet they attempt to bring down the government.
Before the president is able to order the dissolution of S31 and the demilitarisation of Starfleet, he is asasinated by what apear to be agents of another race, but are actually agents of S31. Believing that a demilitarised Starfleet would criple the Federation fatally, S31 believes itself to be in the right and are convinced they are saving the Federation.
Using captured alien ships, S31 and rogue elements in Starfleet begin staging attacks on outposts and colonies, trying to steer the federation into war against a less powerfull enemy.
If the war happens (perhaps its foiled at the begining by the heroes) the Federation becomes more brutal and genocidal. This leads to a split in the Federation where people oppposing the war are deemed as traitors by the new government and rounded up by S31. (who are now being put to work as a secret police force)
We now have a Federation which is becoming more and more like the mirror universe equivelent and a highly militarised and nationalist Starfllet.
With war looming its up to our new crew to somehow restore peace and freedom to the Federation and bring down Section 31 and the new, corrupt govenment.
Hopefully that came out as coherent as it was in my head.
Opinions?
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