The cover is stunning, as is the project page. The interior is beautifully laid out, I love the choice of font and limited use of color. The maps are great but it looks like they were a bit over-compressed when exporting the PDF - it's hard to read the letters/numbers, at least on my monitor.
Breaking the backstory into three parts at different points of history was a great idea, it really helps digest the information. You might consider flipping the Overview and the "Five Years Ago...", "One Month Ago...", "At This Very Moment..." sections, so new readers see the overview first.
I love the idea of an evolving threat, I think you did a great job of making each of Xephion's form interesting. It would definitely keep players on their toes, having to learn new tactics each time they engaged it.
You did a good job of sprinkling the story throughout the adventure, without overloading the reader with too much information at any one time. I liked all of the traps you provided, they could easily be used in any adventure.
The descriptions were vivid but some artwork for the monsters, especially Xephion's forms, could be a nice addition.