For the most part, Neo Arcana follows the planned ending and epilogue 
Brett details in the besm_arcana livejournal.  However, the following 
changes and clarifications apply:

During the battle with the Reversed, Katie kills Yumeka Koto (!Katie), 
and Kyon kills Souichirou Tokuzawa.  Haruko and Satoshi went out of 
their way to keep the number of deaths to a minimum, though there 
certainly would have been more than just those two.

The rift the PCs were sent to seal was the Sword one, largely because 
as unstable as Katie may or may not be, she's more trustworthy than a 
lot of other Swords out there.  (Ryuji was out of commission.)

The player characters save Norishige from suicide after their third and 
final fight with him.  Haruko kisses him afterwards.  Poor Norishige 
ended up being very confused.

Jin kills Sho instead of knocking him out.

Closing a rift involves the destruction of the artifact, so all of the 
artifacts no longer exist.

The prophecy is fulfilled not by all Arcana dying or losing their 
powers, but rather by closing the reincarnation cycle.  Those Arcana 
are the last generation; there will be no rebirth.

The death game with Shun, after the fight is over, involves two cups of 
water: one if which is extremely poisoned.  Haruko drinks the poisoned 
one, but she uses her powers to dilute it just enough to survive - 
barely.