Since you guys have the TR and NC perspective I'll throw in the VS perspective, as I was leading the DIGT platoon in this alert and communicating with other outfits about the alert tactics.
VS started the alert from the south warpgate with a predominant territory advantage in the east (pushing up to, but not in ownership of, Onatha) and a disadvantage in the west (only owning up to Chimney Rock, and not owning Wokuk or West Pass). In the middle we held Raven Landing, Lithcorp Central, and Rockslide Outlook, but TR still had the Ascent.
Immediately we spoke about our alert tactics and goals on leaderchat. We quickly agreed that we shouldn't push our luck pushing the NC more to Onatha as that would only provoke a big response. We knew we absolutely needed Wokuk and West Pass to be able to stabilise our territory percentages and control in both east and west.
We decided to pull out of the eastern lanes, focusing only on defence there, and massively go after Wokuk and West Pass at the start. We didn't care much about the Ascent, although we did make a pass at it to spread the TR forces thin defending three fronts against us. We managed to take Wokuk and West Pass without much trouble. Obviously we were accused much of zerging in the process, but that's to be expected. Try taking West Pass with 50-50 48+ pop within half an hour and we'll talk.
From that point it was mostly a matter of stabilisation. We let the NC in the east push the Onatha lanes down to Splitpeak and Grenade Analysis, but were careful not to lose those bases. We also defended Mekala as we felt that was the most secure spot to hold the NC on that lane. We were careful not to push the NC back from Mekala into Crux, as we saw the NC and TR were fighting close and we did not want to pull away their attention.
In the West we pushed the Wokuk lanes towards Kwahtee, managing to get to Kwahtee Fortress, but all we wanted was to get a few buffer bases there. We constantly pushed for Heyoka, but we were pretty sure we wouldn't take it. Still, it proved a nice population and time sink for the TR who had to come defend with an overpop several times and then wait out the timer we had ticking down to 3 minutes.
This situation marked the halfway point as you can see in the alert stats. We were in the lead at that point and were careful to make sure we could handle being doubleteamed.
The attack from the NC side was focused heavily on Mekala at this point and after a couple of successful defences we couldn't defend it against the massive 96+ pop (like extremely massive, as you said you dumped all your pop into it). This is of course zerging, but with a goal, just as we did in the beginning with Wokuk and West Pass. I don't understand why people don't see this as a simple fact and tactic of the game.
Despite losing Mekala, right afterwards we were able to take the Ascent from the TR, who let us take it for some reason, securing our control of the center bases.
At this point, we had Wokuk, pushing a few bases towards Kwahtee; we were harassing Heyoka (but not taking it); we had skullfuck mountain; we had lost Mekala and were under heavy attack along that lane; we had Splitpeak and we had Grenade Analysis.
Logically, it was clear we had to defend the Mekala lane heavily, and try to be on the offensive on the other lanes. So long as bases are ticking, you can't be backcapped. So that was what we worked on for the remainder of the alert. We never capped another base (except for Silver Valley, where UMVS did a great job), but we didn't lose any crucial bases any more so we had our victory secured. (We lost unessential bases like Silver Valley and a couple buffer bases along the Wokuk/Kwahtee lanes).
I streamed this alert as platoon leader, if anyone is interested you can watch it here.