Oh dear.
I apologise in advance for what is the longest post that I will ever make on these forums. I’ve just been thinking through the ideas this thread’s brought up though, and I’ve come up with a pretty reasonable overall theory that just about explains all of these confusing issues that we’ve been discussing. Some of it will inevitably be wrong, but it’s all inspired by quotes and tangible evidences, so it can’t be all bad. I’d almost finished typing it up as a full-on theory, but I thought I’d edit it and paste it in here anyway to get your opinions.
So for anyone who has the time to read through it, here you go:
And Gehn, I’m sorry, I really am 
[A Theoretical History of Everything That Ever Happened Ever]
As we’ve pretty much established, the Towers’ creators were probably one of the most sophisticated groups of their time. They probably had a global presence too, because it seems that they set up Towers all over the world.
As far as most quotes seem to indicate, the reason that the Towers were set up was to ensure control. The creators thought they knew what was best for the world, and for everyone else living in it, and the Towers were the instruments which would create this balance that they desired.
Now the planet apparently became devastated at some point. It’s unclear if the Towers caused this damage themselves in one of their earlier phases, whilst they were trying to subdue the peoples of the world - the Empire’s assertion that the Towers were continent-burning ultimate weapons hints at this. Alternatively, the peoples of the world might have squandered the planet’s resources previously through war or other wasteful means, as Craymen implies. If the latter was the case, it could be this environmental neglect that angered the Towers’ creators into setting up the Towers in the first place.
At any rate, one of the Towers’ main functions was to repair the ravaged environment, while at the same time they set out to regulate everything else too - including the peoples of the world. We know that the Towers’ creators went into some kind of stasis themselves, which was presumably to await the coming of the rejuvenated world that the Towers would produce for them. I talked about Abadd’s “new way of fulfilling his mission” earlier, which seemed to imply that the Towers’ creators wanted to emerge as rulers over the world.
This is where the Ancients’ plans may have begun to go wrong, though. According to some quotes, the Towers were opposed in the Ancient Age; and the Seekers believed that “dragons ended the Ancient Age by terminating all of the active ruins and towers”. The details of this are obviously hazy, but it does seem that the Towers in the current PD world were never operating at full capacity by default. In all three Saturn games they had to be fully activated before they started churning out monsters and really controlling things. The Towers were still affecting the purification of the environment a bit though, because the Great Fall still happened when they were eventually taken offline. They just didn’t seem to be operating at their full capacity, and for most purposes thay seemed dormant.
That seems to back up this assertion that most of the Towers themselves were forcibly shut down at the end of the Ancient Age, by those who opposed the Towers’ creators. Because of this, it’s possible that everything else went wrong as a knock-on effect.
The problems that arose after this might be due to the Tower programme’s intended time frame.
It doesn’t appear that the Towers’ creators ever planned for the Towers’ programme to still be incomplete ten millennia into the future. If the Towers truly had been damaged or partially deactivated in the past, the plans for everything else might have been thrown out of sync, including the planned operations of Sestren. If the Towers weren’t working properly, Sestren presumably couldn’t exercise its programme of control properly either. And, importantly, the nature of the dragon program might have caused further problems in the unforseen long run.
Now, the dragon program was incredibly adept at destroying Towers and deactivating the Tower network. In fact that was all we ever saw it do. For that reason I’m willing to speculate for the time being that shutting down the Towers was actually its intended purpose.
As we’ve observed, the Sestren system seemed to be a massive interconnected array of programs which individually performed different tasks, and which were geared towards either operating the Towers or providing information which would help the Towers to be better run.
The dragon program was presented just like a component of the Sestren system, and it was also perfectly compatible with the system (as we saw when it eventually gained control of the Towers and shut itself down, taking them with it). On top of this, Abadd happily confused us earlier with the notion that the dragon program was directly related to the Towers’ purpose. This would make sense if the dragon program was a part of the Sestren system, because the Sestren system itself was directly related to the Towers.
Now it’s been suggested that it would be more logical for the primary Sestren AI to have the task of shutting down the Towers itself, but remember that the primary AI didn’t by any means do everything. The system was alive with other programs and entities carrying out different tasks. It strikes me that the dragon program may simply have been the piece of programming designed to shut the network down when the time came.
If the Towers were never going to finish their task, though, there was never going to be a “right time” for the dragon program to be released. Sestren classified it as an impurity and a bug, so it might be that the dragon program was eventually released due to some kind of system error - possibly arising from the simple concept that the Network was never designed to cope with being active for ten thousand years. Conversely, the dragon program was also released prematurely, because the Towers’ task was still not done.
The dragon program’s purpose, then, may have been to deactivate the Tower network so as to hand the “sorted out” world over to the Towers’ creators (who would emerge from their slumber to rule over this changed planet). This could never happen though, because as we know, the Towers were never going to be able to finish their work on the planet. Whatever damage or partial deactivation they had endured meant that their creators’ plans were ultimately ruined.
So the dragon program might have been released in an untimely manner, which would obviously displease the primary Sestren AI massively, because it would still want to try and fulfill its own mission (even if this was more or less impossible given the state of the Towers). As we’ve already established, the dragon program was then ejected from the system, it manually blew up some Towers, it got back into the system, destroyed the AI and shut the Towers off itself. Possibly all because the Ancients simply never planned for these eventualities.
It’s also possible that this is why Abadd could not resurrect his masters, too. If the Towers’ process was meant to be finished long before those ten millennia had passed, then his masters might not have been intended to be in stasis for that long. As Abadd said, “it is too late for my ancient masters” - it’s possible that they had literally slept too long and that their bodies or minds had deteriorated beyond the point of revival.
This also might be the reason why Abadd never woke up naturally: his awakening might have been tuned in to the completion of the Towers’ task, which obviously never happened.
So ultimately, although the dragon program’s purpose might have been to take the Towers offline in order to hand control of the world back to its awakened masters, what it actually accomplished was the exact opposite - it took the Towers offline and handed control of the world back to the human races which the Ancients were so desperate to control.
So, yeah - if anyone made it all the way through that, what do you think?
IMPORTANT EDIT: Alternatively you could replace the whole concept of “The Towers were forcibly made dormant in the past” with “The Towers wore out before they could fulfill their programme”. Those are the two explanations offered, anyway, and they’d both mess up the grand scheme of things just as well
