I know what you’re thinking Gehn: you believe Azel was built to protect the Tower like the dark drone in Panzer Dragoon, yet decided to destroy it.
Craymen says her purpose was to break into the Tower and control it. If she were a willing slave to Sestren/the ancients, she wouldn’t need to break into anything.
Actually no…
I see Azel as the rider of the Dragon protecting the Tower …
And I see Azel herself as a drone that can control the Tower…
[quote=“Geoffrey Duke”]
Craymen says her purpose was to break into the Tower and control it. If she were a willing slave to Sestren/the ancients, she wouldn’t need to break into anything.[/quote]
How do we know Craymen was right about that 
Perhaps Azel saw that her purpose relating to the Towers was no longer valid, now that the Ancient Age had ended.
Craymen also desribes Azel as the weapon built to break into the Tower.
Craymen was privy to whatever knowledge the Empire had gleaned from years of research. The only thing thrown into question here is human interpretation.
So one idea is that Azel was stolen from her creators and masters while still incomplete. Then completed by her captors and asigned the mission of destroying the Tower of Uru. Confused by her own ancient duty, Craymen’s desire to activate the Tower, and the Seekers’ perpetual desire to destroy them all, she decides for herself to do the right thing. Ultimately being its destruction at her hands. Whoever stole her wanted to do the right thing too by removing the ancient monoliths from the world. Azel agreed with the goal, herself.
The other idea is Azel always being meant to control the Tower but deciding of her own volition to destroy it. In this case you must wonder why she was kidnapped at all. She’d just destroy the Tower anyway, even if she was mindlessly loyal to the ancients, right? Wrong. She was taken for a reason.