That’s what I originally thought, too…until you start thinking about where the Heresey program came from. If the Ancients’ plan was as you claim, there would be no need for the Heresey program (nor would there be any rebel factions left to install the program). But since the program does exist, it’s pretty safe to assume that the plan was hijacked by an opposing faction at a time of total unrest, thus allowing the program to merge with the system, unnoticed.
While I do agree that the Ancients did intend to destroy all of their enemies, I don’t think that the destruction of the world was entirely intentional - perhaps they miscalculated the true power of the Towers and after the complete devastation of the planet, they were given a small amount of time to prepare for the future - this would explain why some of the creatures serve no other purpose other than to restore the ecosystem; this would also explain why the main program demands that human populations do not exceed certain limits: the Ancients were making sure that the same mistake could not be repeated…and it’s also possible that by limiting the population, they are also limiting the knowledge available, thus making sure that no one would be able to surpass their technological superiority before their revival.
But, as always, there simply isn’t enough information to warrant one theory over another - that’s the true beauty of this series.
The heresy program could be planted before hell broke loose, near the time Azel was stolen, etc. Just because the dominant faction was going ahead with their plans, it doesn’t mean sabotage missions and other such things weren’t constantly done by the rebels. They could have acted in this way because they realised they couldn’t win and stop the destruction of the world so at least they decided to try and cancel the second part of the plan which would see the main faction return to an oppressed world for them to rule.
I do think the Towers were always meant to terraform the environment but that alone would also make them usable as weapons. Craymen explains that the Towers were built after centuries of warfare between different factions. I’d imagine they were built to repair their destroyed world but apparently the presence of the Towers itself were also a cause for more rebellions/wars so they had biomonsters defend them. Perhaps then the Ancients realized that as long as the Towers were there, there would be people to oppose them. Their plan could have been something like:
Phase 1) Completely destroying their world so nobody remained to stop their plan. This is were the Towers were used as weapons.
Phase 2) Rebuild the world, possibly using drones to maintain the Towers while the Ancients were absent. The biomonsters and dragons remained to guard them.
Phase 3) After the terraforming was completed, activate the dragon that was created to destroy the Towers.
Phase 4) Activate Abadd so he could resurrect the Ancients. The Ancients are back to rule the world with no opposition, the Towers are gone and the biomonsters have been deactivated. All is well.
Now this is of course all speculation but what seemed to have happened was that phase 3 was initiated before phase 2 was complete, resulting in the events we’ve seen throughout the trilogy. I don’t think the Heresy Program itself was altered, at least not in the Ancient Age, but rather some sort of virus in Sestren was hiding and waiting for the right time to trigger the Heresy Program to activate at the wrong time. Sestren realizes this only after the program had been activated/infected by the virus and tries to stop it from completing its mission.
Could have been modified by the rebels rather than planted by them altogether. Could have been like Azel, growing feelings that made him change his mission too. At least I don’t think our characters and Lagi not doing anything much other than getting on for the ride watching the Ancients’ plan destroying itself because of a malfunction.
I can’t recall exactly how it’s presented in game but are we ever specifically told that the Ancients wanted Lagi to destroy the towers? You’d think they could control the monsters and Towers and all their devices themselves rather than require their destruction before they return. So, perhaps the records we have that show Lagi was always meant to destroy them are records from the rebels? Just a thought…
That’s a big part of what does attract me to the idea that Sestren is the template for the Heresy Dragon. It would give a reason for why the Dragon was custom made to infiltrate the Towers, including the power to destroy them if required, but it’s ultimate purpose actually to gain mastery of them. Sestren fulfilled it’s purpose, and perhaps in completely interfacing with the nervous system of the Towers it could not ever be separate again. Somehow it was part of the plan to ‘birth’ a new version of itself, but that one didn’t follow the plan.
Wouldn’t it be amusing if the plan to sabotage and subvert the Towers was itself sabotaged by yet another agenda? I’ve mentioned this before, but there is a single statement that could support the idea, when Gash says that “Dragons ended the Ancient Age”. If we take that together with the idea that dragons were also created to protect the Towers…
Dragons were truly the ultimate weapons ever devised by the Ancients then? Perhaps it was the very fact they didn’t understand the full power of their newest pets that was their undoing?