The Joker could still be a major villain. Even with Batman as a god, the Joker might find some twisted way to challenge him. Maybe he'd try to drive Batman to use his god - like powers in a way that goes against his moral code. Ra's al Ghul could also be a villain. He might see Batman's new godhood as a perversion of the natural order and seek to destroy him.
Well, in 'batman becomes a god fanfiction', the Court of Owls could be a really interesting villain group. They might see Batman's ascension to godhood as a disruption of their long - standing plans for Gotham. They could try to use their ancient knowledge and resources to undermine Batman. Also, Bane could be a villain again. He might think that Batman, with his new powers, has become too powerful and decide to break him once more, believing that no one should have that much power over others.
The Joker could be a likely villain. Imagine his chaotic nature combined with the supernatural. He might team up with a demon to create even more mayhem in both Gotham and Sunnydale. His unpredictable actions would pose a huge challenge to Buffy and Batman.
Lex Luthor could be a likely villain. He's always devising plans to take down the Justice League, and this time he might have come up with a scheme that almost succeeds, until Batman steps in. For instance, he could create a super - weapon that targets the unique powers of each Justice League member.
Obviously, Nightwing himself would be the main character as he's the one taking on the Batman role. Robin, if there's a younger Robin at the time in the fanfiction, would also be a key character. He might look up to Nightwing in his new role or have some doubts about him filling Batman's shoes.
Darkseid is another possible villain. He is extremely powerful. He could send his minions to attack the Justice League first, weakening them, and then use some sort of magic or technology to trap them. Batman would then have to find a way to free the League from Darkseid's clutches, perhaps by finding a weakness in Darkseid's power source.
One likely villain could be Loki. He's always up to no good and loves to play mind games, so a card game would be right up his alley. He might be the one who lures Tony into the game.
One possible plotline could be Batman using his new god - like powers to completely reform Gotham in an instant. He could eliminate all crime, poverty, and corruption with a single thought. Another might be him facing off against other god - like beings from different mythologies who see him as a threat to the balance of power in the universe.
Annabeth would most likely be his ally. She has been with him through thick and thin, and her wisdom would be invaluable as Percy becomes a god. Grover could also be an ally, using his nature - related powers to help Percy in different situations. Another possible ally could be Nico di Angelo. With his control over the dead, he could provide unique assistance, especially when it comes to dealing with the darker aspects of the godly world.
The gorgons could be a likely villain. They might be lurking in the catacombs of Paris, waiting to turn Percy and Annabeth into stone. They could be after some powerful magic item that is hidden in the city.
It could be Danzo. He's always been a shadowy figure with his own agenda in the Naruto series. In a massacre fanfiction, he might be behind it all to gain more control over the Hidden Leaf Village. He has no qualms about sacrificing others for his goals. Also, Kabuto could be a villain as he is a follower of Orochimaru and has his own motives for causing chaos.
DIO could be a likely villain. Since he has a long - standing feud with the Joestar family. He might try to take advantage of the situation where Jotaro and Jonathan meet to cause chaos and try to defeat them both.