The Ending that requires...
Nyx < No companions < No (Win?)< Fight to talk over < Deal < Enter Realm
... results in Apothus Wins NOT Nyx ending
The Ending that requires...
Apothus Wins < Loose < Fight to talk over < Deal < Enter Realm
... has additional choices Accept His Offer/Escape
Escape continues the game until...
...you loose & Accept his Offer / you win & get the Apothus Wins ending.
Accept his Offer results in the Apothus Wins ending (Memories of Apothus)
(I'm using the steam version btw)
Viewing post in Dawn of Corruption 0.8.1 Release Notes comments
Same here, I'm playing on html, I usurped Apothus' cult and defeated his second form but it just proceeded to the Incomplete Ending without any option to merge with Nyx (no companions as well) unless the 'No' branch after 'Fight to take over' doesn't mean winning the fight...which makes me wonder if there's something else that needs to be done to trigger the Nyx Ending