According to the most recent news, Episode III takes place one year after the previous installment. Shion has quit her job at Vector because she believes that Vector is somehow behind the gnosis phenomenon, and has joined up with the organization Scineta (Scineta was founded by Meris at the end of Pied Piper). She later learns that the KOS-MOS project has been scrapped and another android, bearing a striking resemblence to KOS-MOS, named T-ELOS appears.
Additionally, Episode 3 is being called the "conclusion of the Xenosaga series trilogy." It is uncertain whether this reffers to the series as a whole or just the conclusion of the current story arc (making it the first trilogy). Some speculate that the meaning is intentionally ambigious and that the future of the series is heavily dependent on how well the third installment sells.
Links
Official Site: http://namco-ch.net/xenosaga3/index.php
Famitsu Scans:
Page 1
Page 2
Translation of Famitsu Scans: (based on earlier, lower-quality scans, not all of it was ledgible so not all of it has been translated): Linky!
Gamespot Trailer: (Higher quality video, requires registration/login to download) Linky!
1UP Trailer: (Lower quality video, slightly different content): Linky!
And lastly, here's the news dump topic on my BBS (I made it mainly so I wouldn't lose the random things I was finding), I think I covered most of it here, but just in case I missed something, here it is: http://www.shojokakumei.net/SKBBS/viewtopic.php?p=1183
I know there's already been a discussion topic started (you can find it here: http://www.gaiaonline.com/guilds/viewtopic.php?t=1293654 ) but I stareted this one more for formality's sake (so it works with my system of organizing news). So feel free to either discuss here or in the other topic.