I HAVE MORE CONSPIRACY THEORIES, BRACE YOURSELVES.
[spoiler=Theories]
[spoiler=Mikoto]
She is not truly dead but rather faked her death in that explosion in order to rile up her child's power before the war.
1.Considering that she did this and that with Hydra, it's not really strange, (Wait, which of the dragon is Kamui's daddy? It's Hydra right? Whatever you get it.)
that she would actually sides with the dragon in term of game plot. And when Kamui didn't do as Mikoto wanted, she figured she'd show up in front of him/her and rile them even further to let their guard down before killing them.
Or...
2. She had to disappear to hide herself from Hydra and would show in front of Kamui when the time came to aid him/her against the Invisible Kingdom. (First one is more likely considering Kamui is holding her at sword point.
[spoiler=Hoshido Daddy]
Assuming Mikoto is the first point, she would resurrect him after her supposed death and make him a minion of Invisible Empire, seems fitting.
[spoiler=Gunter]
SHIT'S CRAZY YO.