Okay, so I've read all the way through to chapter 30, and...I'm utterly lost. Did Kon get ejected from the virtual reality? And all the stuff with Toki is a flashback, right?? PLEASE help!!

Well, actually im utterly confused too. I just looked it up and well, eveybody is confused as to what is going on. (But from what I understand they aren't really flashbacks because toki isn't really "remembering" them... it like a recap to better understand the story kinda i guess... ) The most recent chapters are the events before Toki failed history and went into that virtual reality thing. That chip (if you read that far yet) they are investigating has something to do with the virtual reality itself. So basically, I read that volume 6 and 7 are taking place before he is sent to the virtual reality and in a couple of chapters it will go back to the main storyline.
Here is a link where someone asked the same question(there are some spoliers btw)

http://community.livejournal.com/amatsuki_manga/116459.html

And about Kon, i guess he just lost his memory... (if you go down a little futher on the page on the link I gave you, he/she said everyone except Toki, Bonten, and Tsuyukusa lost the memories and were "reset" )

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Why, hello there!!!

I watched the anime and it really helped. I suggest you read very very carefully
I missed a page and didn't know a thing that was happening so I had to re-read it. as far as I know the 'gods' changed everyones memorys because of the priestess or something like that
and of course Toki's not affected

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I hear you say "Why?" Always "Why?" You see things; and you say "Why?" But I dream things that never were; and I say "Why not?"