QUOTE (Asuka)
as well as how Episode 3 ended.
Shion's arc has finished but the series is still open for more episodes.
*Episode III Ending Spoilers*
KOS-MOS and chaos survived and live on in one form or another. Although the human race is till alive things aren't looking too great as the whole way of living has been distorted with the loss of U-DO. We don't know what happens to any of the characters really and more adventures can still be had.
Ziggy, MOMO, Jr and Shion are finished with basically... but chaos KOS-MOS and Jin (possibly) seem to be about to start a new adventure. Yes I know Jin died but I don't think that's the end for him (death doesn't mean much in xenosaga anyway)... there is a reason I think that but it's been a while since I've seen the ending so I can't think why.