I don't really find it so shocking at all, really. In the end he was, or is, the Azure Dragoon. When you confront him and he takes on the power of Nidhogg it implies that there's some serious corruption there. Afterwards you channel the Dragoon's power and defeat him by throwing a column of flame at the guy in which he promptly disappears.
So either one of two things is happening here in my opinion:
1: the MSQ takes place before the final lvl 50 Dragoon quest.
2: You defeat Estinien and he returns after his sound thrashing, gets taken in by the Temple Knights who, by all appearances, need every edge they can get against the Dravanians and he IS the Azure Dragoon after all, and disguises his 'bond' with Nidhogg as "the eye is talking to me and grants me some power blahblahblah I can hear his planz"
Anyway it speaks more of Ishgard's desperation for powerful allies to me. It also has an interesting hook in that Estinien will either have the chance to redeem himself or to succumb fully into being a monster. Either way you as the fellow Azure Dragoon/Warrior of Light will be there to help or hinder him.
So either one of two things is happening here in my opinion:
1: the MSQ takes place before the final lvl 50 Dragoon quest.
2: You defeat Estinien and he returns after his sound thrashing, gets taken in by the Temple Knights who, by all appearances, need every edge they can get against the Dravanians and he IS the Azure Dragoon after all, and disguises his 'bond' with Nidhogg as "the eye is talking to me and grants me some power blahblahblah I can hear his planz"
Anyway it speaks more of Ishgard's desperation for powerful allies to me. It also has an interesting hook in that Estinien will either have the chance to redeem himself or to succumb fully into being a monster. Either way you as the fellow Azure Dragoon/Warrior of Light will be there to help or hinder him.
