General story has a much darker tone, Eris is a permanent enemy rather than an eventual ally, Nowe is a darker character who has to confront conflicting feelings of love andd hate for Caim due to being the "child" of Furiae and Inuart, Urick possibly being gay is more overtly expressed in a crush he develops on Nowe, and Nowe's latant power as the New Breed gives him the ability to cancel out pact-like magic including genuine Pacts and the Seals; this gives Nowe the option of saving either Urick or Caim or both during the story. Now for the adjusted endings:
1; Ending A - Same as in original game (Legna dead, Seal System restored with Eris as the new Goddess), but with the added dark elements from the later novel expansion.
2; Ending B - Same as original game, with the added layer that comes from Eris and Nowe actually hating each other and being forced to work together to fight a potentially futile war with the Gods and Watchers.
3; Ending C - Same as original game, but the severing of the bonds between the Gods and Midgard doesn't just take out the Watchers and Dragons, but anyone with connected magical abilities, so Seere and Nowe both die. Eris and Manah are left alone in a peaceful yet shattered world - Manah is left broken by the loss of the man she loves (Nowe), and Eris faced with rebuilding a world that now hates the Knights of the Seals.
4; New Ending D - If Nowe saves either Urick or Caim, he discovers his power to break pacts and Seals, and events play out in a similar manner to the revised Ending B, but when he enters the Dragon's Bone Casket, it instead accepts him and he is granted powers equivalent to the Gods. Using these, he remakes the Seal System with himself as its sole guardian "God", and makes either Caim or Urick his immortal servant as he becomes the effective ruler of the Dragons and humanity. This would end with a final cutscene showing Nowe leading a successful campaign with Manah and Nowe's chosen servant against the Watchers and Gods, and even across into other realities.
5; New Ending E - If Nowe saves both Urick and Caim, during the severing of Caim's pact, Eris attacks and Manah holds her off, but a final burst of flame from the dying Angelus kills both Eris and Manah, leaving Nowe in a fragile state. Events then play out as in Ending D, but Nowe instead becomes a monstrous dragon-Watcher hybrid due to his despair at losing Manah, and Caim and Urick are forced to kill him. Legna declares the experiment a failure and chooses the lead the Dragons in a final campaign against both the Gods and humans, while Caim and Urick decide to mount a final desperate crusade against the Dragons, possibly considering allying with the Gods and submitting to their will to ensure their joint survival.