Federation Civil War

The Federation Civil war was a major war lasting two and a half years from mid-2405 to 2408, during which the Federation declared open war against a group known as the New Insurrection and their allies, the Maquis remnant.

Prelude
Recently having entered the 25th Century, Edward Shield and Lianna Young met with top members of the Federation Council and Starfleet Command, addressing instances of corruption they saw within the Federation. Their concerns were dismissed and the two captains were told to keep their mouths shut and not "rock the boat". They refused, later being attacked by Starfleet Security on their way back to their ships.

Open War
In 2405, the Federation President reinstated Order 865, which made the ship and crew of the USS Enterprise (NCC-1701-C) and USS Admonitor enemies of the Federation. Ships were reassigned from year-long-missions to hunt down and destroy them. It was during this time that the Insurrectionists made an alliance with the remnant of the Maquis.

Checkmate
Towards the beginning of 2406, Edward Shield began suffering the affects of a rage virus that mentally unhinged him. He was captured by the captain of the USS Titan (NCC-80102), Will Riker and it seemed that the conflict would die down without the ring-leader of the "insurrection".

Interim Conflicts
In 2406, war once again erupted into utter hatred when, in mid-2406, the Insurrectionists stopped key members of the Federation from entering The Higher Plain, in actuality a ruse by the Founders to enslave the races of the Alpha and Beta Quadrants.

Second Galactic War
The Federation began splintering toward the end of 2406, with the factions kept in check through secret fear of Admiral Nechayev. This balance of power ended on New Year's eve of 2407, when the InterGalactic Relon Empire besieged Earth, killing almost 30 billion. A mutual alliance was caused between the New Insurrection and the Federation to counter the Relon invasion, as well as a new threat from the Ultari Empire.

Though the threats were assuaged for a moment, the election of a new president saw Alynna Nechayev rise to ultimate power. She outlawed all religion within the Federation and declared the New Insurrection enemies, thus resuming the state of "conflict".

Conclusion
A great blow to the Federation came when K'hallA, a member of the New Insurrection, successfully led the Klingon Empire from the Federation, thus causing the Federatio to view the Insurrectionists as a serious threat. However, with Starfleet in tatters from repeated assaults by the Ultari, Borg, Relon, Dominion and Children of Khan, they were in very little shape to be lending large amounts of ships to hunt the two ships.