Maybe a new villain created by the combination of Naruto's and DC's worlds. A powerful ninja - like figure with the ability to control technology. This villain could be after a powerful artifact that Batgirl is protecting and Naruto is also interested in for some reason. He would be a formidable foe as he can use both ninjutsu and high - tech weaponry against them.
The main antagonist could be a powerful demon from Naruto's world that has possessed a powerful DC villain like Ra's al Ghul. This possessed Ra's al Ghul would have all the knowledge and resources of the League of Assassins as well as the demon's dark powers. Batgirl and Naruto would need to find a way to exorcise the demon from Ra's al Ghul and stop his evil plans for both worlds.
It could be Orochimaru from Naruto's world who has found a way to cross into the DC universe. He teams up with some of Batman's villains like the Joker. Orochimaru wants to use the chaos in Gotham to conduct his dark experiments and the Joker just wants to cause mayhem. Batgirl and Naruto would have to deal with Orochimaru's snake - like attacks and the Joker's unpredictable madness.
It could be a character like Orochimaru who somehow gets access to Gotham's technology and becomes even more powerful. He could be creating new types of jutsu using the advanced tech there and causing chaos in both worlds.
It could be Darth Sidious. Since he is always looking for power and control in the Star Wars universe, he might see Naruto as a threat to his plans when Naruto arrives in Padme's world. He would try to eliminate Naruto and use Padme as a pawn in his political games.
It could be Ra's al Ghul. He's always interested in things that can give him an edge in his quest for immortality. If he discovers the power of chakra in the Naruto world, he might try to take over both worlds. His skills as a master assassin and his vast resources would pose a huge threat to Naruto and Batman, who would have to put aside their differences to defeat him.
A powerful dark ninja who has made a pact with some dark force from another dimension. He sees Gabriel as an intruder and Naruto as a threat to his plans of taking over the ninja world. He would use his dark jutsu and the power from the other dimension to oppose Naruto and Gabriel, and would stop at nothing to achieve his goals.
It could be a powerful ninja from Naruto's world who wants to use Nobunaga's knowledge for evil purposes. This ninja might see Nobunaga as a means to gain more power and control over the ninja clans. He could try to manipulate Nobunaga into starting wars between the clans by using his strategic mind in the wrong way.
The Akatsuki as a whole could be the main antagonist. They might target Naruto as usual, but now with Kabuto on Naruto's side, they have to deal with both of them. The Akatsuki's various members with their unique abilities would pose a great challenge for Kabuto and Naruto to overcome.
It could be an evil ninja from Naruto's world who has somehow gained the powers of a DC super - villain. For instance, Orochimaru could merge with Lex Luthor's intelligence and resources. He would be a formidable foe as he combines Orochimaru's snake - like abilities and knowledge of jutsu with Luthor's strategic mind.
Perhaps an evil ice mage from the Frozen world who has heard of Naruto's power and wants to steal his chakra to become all - powerful. This mage could be jealous of Elsa's natural ice powers and sees Naruto as a means to an end to get rid of her as well.
It could be a combination of villains from both universes. For example, Orochimaru from Naruto could team up with Salem from RWBY. Orochimaru is interested in the power of the Grimm and Salem wants to learn about the power of chakra. Their combined evil could be a huge threat to Naruto and Neo, forcing them to use all their skills to defeat this powerful alliance.
Perhaps an evil organization that wants to harness the power of both Naruto and Nero. They might see Naruto's chakra and Nero's Devil Bringer as the keys to ultimate power. This organization could be led by a powerful sorcerer who can manipulate dark magic and has minions from both worlds at his disposal.