GDI has gained quite a big advantage overtime after the victory in TWIII.
However, unlike TWI or II, Nod has not gone completely into hiding - as Kane is still alive and well, and GDI is busy with a new threat.
The sped up spread of Tiberium, and the return of Tiberium-based lifeforms. (Unlike the actual C&C 4, the overwhelming majority of the world is not a giant Red Zone. More like 60%, with Blue Zones being 10%.)
GDI comes up with the concept of a (much weaker) Tiberium Control Network, but requires Nod's excessive research on Tiberium. GDI High Command proposes a short-term alliance, agreeing to provide territory and basic technological support, in exchange of Nod's aid on the TCN - which, unlike in C&C 4, is not powerful enough to cleanse the whole world. It was only meant to keep Yellow Zones yellow, and Blue Zones blue.
Nod agrees to help, as Red Zones are not a very useful asset to have. They cannot support human population, are full of dangerous Tiberium life and are generally not a nice place to be in.
Or at least they seemed like they did.
Everything goes from bad to worse. Kane and the Brotherhood instead sabotage the peace meeting and destroy the GDI HQ, killing everyone inside.
The resulting chaos amongst GDI would be a big disadvantage for them, and Nod would be free to emerge once more.
The GDI campaign consists of you, one of the last few commanders remaining after the absolute destruction of the GDI HQ, trying to push back Nod's assault on the last few blue zones remaining while also fighting off Tiberium lifeforms. You will also try to complete the TCN.
In the Nod campaign, your mission is to wipe out GDI off the map and defend against Tiberium-based mutants, just like GDI. But of course, your most important mission is to activate the Tower and ascend.
The ending is a touchy subject, but I would probably go with something along the lines of the TCN being succesfully activated using stolen Nod technology (Presumably one or few GDI and Nod mission(s) related to this too), but also causing a reaction from within the Tower, showing that the energy caused by the TCN is able to potentially activate the Tower and make way for ascension.
Nod will then try to assault the core of the Network and overcharge it, activating the Tower but destroying the entire Network.
The GDI ending implies that the battle at the TCN core ended with GDI being the victor,
The Nod ending, I can't really decide. I kind of want the Nod ending to be the "bad" ending and different than the C&C 4 ending, but that also conflicts with the purpose of the Scrin Towers. So, I made two versions.
1- With all of Brotherhood now ascended, the technology that would be required to rebuild the destroyed TCN is now gone, thus forever dooming Earth to a Tiberian life - that, or a massive Scrin invasion.
(The justification for this would probably be that because the Scrin mining operations have ended, the Tower has no place to send the Tiberium to - but it is still linked to other locations. And I don't think Kane would want to go to a mere Tiberium storage of the Scrin, so...)
2- The Scrin Tower is succesfully activated, and Nod has ascended. However, the final outcome is much different than what GDI has anticipated. The activation of the Tower caused Tiberium fields all over the world to dissipate, effectively purifying Earth.
However, the Scrin invasion is still on the horizon...
(This ending can probably be justified easily, but it also makes GDI look like total fucking idiots for almost dooming the entire planet.
Overall, I prefer the first ending.)
...But most importantly, I would get rid of the emotional wife bullshit. Maybe even put the player in the shoes - well, circuitry - of LEGION once more for the Nod campaign.
So there. You just read a wall of text of me getting carried away with this whole thing.