The Federation Civil War encompasses the in-fighting within the Federation that resulted from the decimation of the Infection, a nanite-based virus that attacked anything and everyone in its path. The Federation split into three distinct factions:

  • those that supported the original Federation
  • The One True Federation, a front for the Equity Corps, under the auspice of President Sebastian Cross
  • The Confederation of Planets

Starfleet forces became split between the various factions, and it meant starship went up against starship. The civil war lasted for years, before a final conflict in orbit of a pre-warp planet, Rifkin IV. After this time, the in-fighting eased off as the various factions turned their attention inward and began rebuilding themselves. (Star Trek: Lost Frontier)