Character Developments (Spoilers)

     The fragments of Hojo's digitized mind managed to spread into parts of Weiss' body, effectively controlling him.  Hojo then had the Deepground SOLDIERs to abduct those that don't have Geostigma to help Weiss absorb Omega and fool the planet into summoning it.  The mako-influences further enhanced Weiss' abilities and made him far stronger than Vincent.  But Vincent was able to defeat Weiss by using his Chaos power.  After being defeated, Nero merged with Weiss.  Hojo warned them to stop as they won't be able to control Omega as a result of an impure being inside of Weiss.  Hojo was finally destroyed as they merged together and this evoked Omega's power.  Weiss is later killed by Vincent in his Chaos form but Weiss' body is carried off by an awakened genesis.  There were still some questions left unanswered at the end of the game.