At first you say that they are given clearance level 1 for Protocol-898-01-2, then later you say they are given clearance level 0.
The way that you partially describe the circumstances to enact each protocol and almost describe them twice is hard to follow. I would suggest changing it to be linear. - This is when you enact it, this is what you do. I get a little lost in how you mention Protocol 898-01-1, Protocol-898-01, Protocol-898-01-2 and Protocol-898-01E-02 the way that they are currently described. It's fine having longer protocols, but they way that they are structured currently makes it harder to follow than necessary.
The list that you have detailing the specifics of when RPC-898 will combat should present like below, as right now it reads strangely.
and as such will only engage opponents that are:
1. Are knowledgeable in at least one form of the combat as the RPC-898-01 instance.
2. Are in possession of the same or similar equipment of the culture RPC-898-01 originates from.
3. Only combats the Engage the RPC-898-01 instance in a duel.
I'm glad you included logged instances! I had been hoping for something like that in the article. I also very much liked the poem at the end, that note really helped to tie in a story to this entity. I think this still needs a little work to iron it out, but the ending made it much better.
