Daijirou is defo the main antagonist
An interesting declaration, but I will respectfully disagree. I remember her mission was to stop the new demon king, and she's taking Miri with her for Miri's insight.
Beyond that, I don't think she'd store her documents in the floor unless she wanted them discovered (she has an airship to keep important data), so it's probably something she wanted found in order to prevent whomever did that research from succeeding while she's trying to stop the new demon king.
The antagonists in this story seem to be the older hero and the new demon king... as well as whomever possibly murdered that one old god (potentially someone who roams the universe that myworld is from). It seems, to me, that this is heading towards 3 fights: Miri takes on the new demon king, the new hero joins Daijiro and takes on the old hero, and our main character against the god killer.
At least, that's along the lines of where I would take it if I were the author.
Also, there's still a huge mystery as to why this isekai world is teleporting people before they die instead of reincarnating souls like they're apparently supposed to.