I haven't been on here for a while, so I just saw this.
When it comes down to the story, I always refer to dotswarlock for the story itself and the eventual ending, which is happy for the humans.
A summary of dots'
Before and up to WWII. Seraphim observe humans and see them as a species that evolves faster than anything else (in terms of technology) but they also see how willing they are to accept the consequences of what they do (pollution, war etc). They give up on the humans after the nuclear bombs destroying Nagasaki and Hiroshima.
Somewhere between WWII and the discovery of the Seraphim by humans: seraphim discover the quantum realm, a place where the change in energy would allow you to live indefinitely and see two options.
1. The quantum realm is an evolutionary dead end.
2. Not going to the quantum realm is to refuse to evolve.
The Seraphim can't decide on which path to take and go to war (as this was something they have learned from humans).
Pretty much the entire galaxy is ravaged before they decide that each Seraphim can choose as they want. Those who want to go to the quantum realm go there (build the gateway on Alpha 7). Those who don't stay behind on one planet (Seraphim II).
Fast forward to Black Sun being fired (in dotswarlock's it's a combination of several victories. The Avatar of War is killed by an unlikely alliance and the princess spreads the message of peace): QAI (already under control of the Seraphim) opens the realm to the quantum gate and lets a load of Ahwassas in.
The Seraphim make some people on the Aeon their puppets, creating the order. Shortly after arriving, they attack the Cybran Nation, which has its military completely devastated. This happens in Dots' 6th book.
The UEF and Cybrans form an alliance, and eventually allow the Loyalists in as well (books 7 and 8). Meanwhile the Seraphim are as unstoppable as in book 6.
Book 9 goes on about using Seraphim tech acquired (in book 8), this gives an explanation in the complete rebalance between original SupCom and Forged Alliance. Book 10 is the timeline from the 4th mission to the last of Forged Alliance.
After book 10, the remaining Seraphim are in hiding, mostly because they are now at a disadvantage in numbers and eventually technology.
In that setup, you could actually change the balance of missions to make the game reflect the broken balance. However, this is more of a challenge for the alliance than the Seraphim, since they're so much stronger than the humans in books 6-8.
What you could do is make a Seraphim vs Seraphim mission in their own war (quantum realm decision), and stuff after book 10.
A mission for book 6 could be: Attack and destroy a Cybran settlement, in which you're severely outnumbered but your own weapons are so much better (dots made the seraphim ACUs have insane regen vs the firepower of other weapons and made them invulnerable vs the ML,GC and CZAR laser, he even got the ML to blow up because of its own laser instead).
Anywhere between 9 and 10 can be regular missions. Maybe a prelude mission for the seraphim to the game's mission 2. There the Loyalist movement had spies in the order, which were detected. Then an entire operation was endangered. Simple mission: attack and destroy a Loyalist settlement before a timer runs out (i.e. before they power the quantum gate to evacuate the settlement, you could possibly change the timer's pace by the number of power generators they have).