Main factions provide most of your army along with faction talents and topbar abilities.
This is the majority of your army, your faction-wide talents, and topbar abilities. When playing ZeroSpace you also have a mercenary faction to supplement your army as well.
There are 4 main factions, 3 of which are currently playable:
Grell - Insectoid and arachnid aliens using bugs, plants, and nature.
Legion - Religious fanatics with low-level troops eager to die for powerful commanders.
Protectorate - Humans who fight for colonies throughout the Orion sector.
Xol - Shapeshifting robots with the ability to merge together.