where do you recommend we start for the false prophet files?
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The way the FalseProphet-HQ website was set up was unorthodox. Each webpage acted as its own 'separate' thing and the only way to get to the next page was via the puzzle.
Of course you could have downloaded the files and dug through them for the links to the next webpage and through there you can start to structure the website in some way.

The original appearance of these files were links that would look like the following: http://falseprophet-hq.com/room666
Because these are the downloaded files for those links you will see them listed as something like this instead: room666.swf
In the source code for some pages there were links to other parts of the website/puzzle with the most reoccurring links being the following:
/room15
/room16
/room17
/room51
/room61
/room71
/room666

If you haven’t noticed already the first six rooms are reversals of each other while the last one is like a 'hub' that connects all the rooms. There is a reason for this.
There is a correct order to go through the site at first but if you want to look through those links around the same time then go ahead. /room1 is also related to that group.

The files titled login.swf, login-level2.swf and issueX-level19.swf all had 'countdowns' that would have been previously one of the first things you saw when you opened up the front page of the website.
The very first one that you would have seen at one point is login.swf so if you want an absolute place to start then start there.