The concept for the UNE was simply an evolution of the UN as humanity began colonizing the solar system. The various factions (Lunar Republic, PRM, etc) were in defacto existance right up until intrasystem subspace (NOT NODES) was discovered, at which point the UNE tried to enforce their policies on everyone. They didn't like it.
By the time the Unification War occurs, there has been several wars not just against the UNE but amongst the other factions as well. In the campaign, the Lunar Republic and PRM (People's Republic of Mars) are feuding and this spirals out of control and drags the other factions in resulting in the U-War.