First of all, one of the things about Nod is that them being the threat they have been in this quest post-TW3? That is
extremely different from how they normally have been. Pre- and Post TW1, Nod basically hid as part of the normal population, rogue countries and countries that weren't particularly co-operative towards the UN and superpowers. This might have changed, but by the time it would have human civilisation was rapidly collapsing as tiberium started spreading everywhere like crazy throwing everything into chaos. So GDI was too busy creating a global government from scratch whilst keeping as many people alive as possible to go hunting Nod. Remember, GDI only became an actual government and military rather than a Joint UN Security Council Task Force sometime in the late 2020/30s which means they absolutely couldn't just wipe out Nod and all their supporters or the governments ordering GDI to do that would have been overthrown.
As things calmed down to the point that GDI might be interested in destroying Nod if they were a danger, Nod had created a widespread
global tunnel network. So yes, building a lot of underground infrastructure fast and relatively cheaply is actually more or less a 'solved problem' in the C&Cverse. Also Nod at this point looked more like a bunch of warlords using the Nod from the 1st Tiberium War as a source of legitimacy, not the persistent and widespread faction we know them as. Then along came the 2nd Tiberium War where people start realising that not only is Kane still around, but the Brotherhood of Nod may actually be more of a reality than anticipated.
However, post 2nd Tiberium War Nod again basically just collapsed into a massive number of local warlords all over the place that were controlling the territory that GDI didn't see any need to claim. GDI of course was more cautious this time because they'd seen exactly this pattern happen before, and they got stabbed in the back by Kane for ignoring the danger it could become. So they sponsored a lot of Nod warlords which were perfectly happy to take GDI's resources for crushing their local competitors that might actually bother listening to Kane whenever he popped up again instead of stabbing him, tossing the body into an unmarked grave and enjoying being the local power in the regions which had been left abandoned after the national governments collapsed.
Only along comes Kane and he spends the decade or so before the Third Tiberium War killing off the warlords which wouldn't backstab GDI when he ordered whilst stealing or developing tech and building up the more overtly Nod Loyalists in regions away from GDI's precious Blue Zones so they weren't seen as a threat worth worrying about. Sure, Nod could no longer build everything underground due to the fact that tiberium's spread meant anything underground would soon collapse or be consumed by it, but that's what the stealth fields are for. Then he decided it was time for TW3 to happen which saw all the parts of the Brotherhood of Nod come together and attack in ways GDI was completely blindsided by.
Now we come to what we see in-quest. And everything is completely different for three reasons. The first reason is that GDI's sick and tired of counting the global organisation needed for Nod to be a threat to them down and out for the count only to have it pop back up a decade or two later. So they're going to crush any organised Nod Warlords they can reach whenever they can. Secondly is that the post-Liquid Tiberium detonation mutation of tiberium and mass expansion of the Red Zones hasn't slowed down. Which means the vast swathes of land between GDI's borders and the Nod heartlands are disappearing as Nod gets pushed closer and closer to the Blue Zone borders as they were at the end of TW3. Finally? We as GDI were actively pushing out into the Yellow Zone border regions and
staying there unlike any time since the post-TW1 government collapse saw GDI pulling back to the regions which would become the future Blue Zones.
So as Nod is getting pushed towards us, we're pushing towards them. And every single Nod warlord knows that individually, they can not stand up to the global juggernaut that is modern day GDI even when we were on the ropes right after the war. After all, it's not like Nod was any better back then, and GDI's got the advantage of being a global power to boost the rate at which their industry recovers. So all the Nod warlords realise that unlike before, they can't just ignore each other, try to give GDI a few targets to vent themselves on that don't hurt their forces and crush all other power blocks in the local region to rule the roost. GDI's thrown that playbook out after all. So they have to co-ordinate on a global scale like usually only happens during the Tiberium Wars in order to make up for the lacking industrial and research capabilities they individually and also collectively have compared to GDI.
It's the only way they'll survive.
As for why GDI doesn't just wipe them out now... Well, the modern GDI is actually trying to honour the
Global Defence Initiative part of their name, which means they can't just kill off hostile civilians because they're near a military or joint use facility. Also, GDI would really like to keep as many of those people and even the Nod combatants alive as possible because the human population has crashed
hard and is still plummeting even if it's slowed down. So every dead person that they didn't actively have to kill
right then is more population to hastening the recovery of humanity's numbers once the whole 'tiberium trying to eat us all' issue is either solved or sidestepped. Also again, Nod is extremely good at the passive and active stealth measures so unless we get actual boots on the ground and eyes on target we can't be sure we're actually bombing anything more than funnily shaped painted rocks...
