Allegiance

From http://en.wikipedia.org/wiki/Microsoft_Allegiance:
Allegiance is a multiplayer online game providing a mix of real-time strategy and player piloted space combat gameplay. Initially developed by Microsoft Research, the game was later released under a shared source license in 2004 and is now maintained and developed by volunteers.

The story in which the game is set takes place circa 2150, shortly after the destruction of Earth by an asteroid. This cataclysm forced the remnants of humanity to the stars in search of new land and resources. Humanity quickly fractures into four main factions:

The militaristic Iron Coalition, descendants of a United Nations-sanctioned peacekeeping force.
GigaCorp, a transplanetary corporation bent on controlling all natural resources.
Belters, a motley collection of traders, freedom fighters and pirates.
and the Bios, a mysterious off shoot of genetically engineered humans with their own agenda for "stalegenes".
In the midst of the ensuing civil war, humans discover the alien Rixian Unity. An ancient and advanced race, the Rixians seek to "enlighten" heathen races (such as the human race) and convert them to their religion.

Allegiance was first released for multiplayer on the Microsoft Zone under the name Allegiance Zone. This was a paid subscription service but free play was available on the Free Zone (which had fewer features). The game never achieved commercial success however, selling a mere 29000 units in the first year of release[9] and the official servers closed in 2002. During its brief retail life Allegiance had drawn a dedicated following that continued to play beyond Microsoft's discontinuation of support for Allegiance. Players created their own utilities to enable them to connect to LAN-hosted game servers and continued to play.

Allegiance is still maintained by http://FreeAllegiance.org, where the client can be downloaded, and played multiplayer online for free.