A mention of attacks being conducted via gate hacks paid for by credits made me think of the end of the Cybran campaign in the original supcom. In that ending the Cybrans take control of Black Sun and fire it, unleashing a virus into the quantum network that destroys the quantum gate network and disrupts quantum communications, buying at least 20 years for the Cybrans to build up before the network is repaired and the war renewed. Since I didn't notice a particularly detailed rationalization of the Galactic War lore wise, what if the game takes place in an alternate reality of the game universe, in this case the Cybran canon.
Say it goes like this: The Cybrans defeat the other factions in the struggle for Black Sun and fire it destroying the Quantum network. This of course is ruinous for all quantum based communications and as a result when the Seraphim storm onto Earth through the Quantum Rift and level the earth by Ahwassas news does not spread fast. Each faction has its tips on the Seraphs arrival though; for the Aeon it is a cryptic warning from the Princess (also since the Seraphim are unable to use the Quantum network for communications the Order of the Illuminate never forms since it partially was a result of a loss of the Princess's leadership when she was thought dead and the arrival of the Aeons' gods). The Cybrans have QAI's betrayal (he would probably attempt to kill Dr. Brackman in his lab somehow and fail as proven by Brackman's later presence). And a further note on the QAI subfaction is that it would be weaker since QAI is a creature of the Quantum network and would be crippled by its near destruction. The UEF have broken communications from Earth and may have one or two space ships as evidenced by the events of FA's credits.
However while Brackman's virus caused incredible travel disruptions with enough energy it's still possible to gate a limited amount (it's a rough ride though). As a result isolated sections of each faction meet the Seraphim and encounter their superior technological might and taste for destruction of all things human (I say "superior" technology because it did advance between vanilla supcom and FA and if you mean to tell me that the balanced version of the Seraphim could become the terror of the galaxy after gating from Earth to attack planets held by heavily entrenched commanders from all factions you're crazy). This forces the isolated factions who are near the Seraphim to band together in an alliance forged mainly by a common foe and through a series of costly battles manage to steal enough Seraph technology to create a balance.
Meanwhile the main body of each faction are working to reassemble the gate network and still nurse all the hatreds that had fueled the war for a thousand years. As a result as gates are rebuilt each faction came back into contact with each other and hostilities reignited. All told it takes 15 years before firm contact is established with the core systems (I.E our solar system) and 20 to reconnect it with the rest of the network. Meanwhile the Nomad Hegemony with their space ship advantage has been watching in interest as those who exiled them reconstruct their pathetic gates. Deciding that the best way to punish them is by making sure the Infinite War is continued the Nomads discreetly offer their service to all factions as mercenaries, they're always careful never to show their full strength. When necessary they intervene to keep the flames of war burning.
When the Alliance with their balanced technology (meaning on par with the Seraphim) and camaraderie with each other are contacted they are ordered back to their own factions and their positions are taken over by commanders with old tech ACUs that the Seraphs easily overwhelm, giving them a strong foothold in our galaxy. Meanwhile the alliance members are buried in a bureaucracy in each of their factions that ignores their pleas to unify but takes advantage of their technology to modernize the war machines used in inter-factional war. QAI, the Seraphim, and the Nomads all grow steadily in strength as humanity works to destroy itself.
And that brings us up to the setting of the Galactic War Game and why there is no evidence of inter-factional cooperation or the events of the Forged Alliance campaign in the game play.