It could be a new character, perhaps a powerful wizard from a far - off land who wants to take over both Donkey Kong's jungle and Mario's Mushroom Kingdom. This wizard has the ability to control the elements and uses this power to create chaos, forcing Donkey Kong and Mario to put aside their differences and fight against this common enemy.
Bowser could still be the main antagonist. He might see Donkey Kong and Mario teaming up as a huge threat to his plans of taking over the Mushroom Kingdom. So he devises even more devious schemes to stop them, like creating new types of minions or using powerful magic artifacts.
Maybe King K. Rool from Donkey Kong's world decides to team up with Bowser. They combine their forces and resources to try and defeat Donkey Kong and Mario once and for all. Their combined strength and cunning would make them a formidable antagonist, and Donkey Kong and Mario would have to really work hard to overcome them.
One possible plot could be that Donkey Kong and Mario have to team up to save the Mushroom Kingdom from a new, powerful villain. They combine their unique skills, like Mario's jumping and Donkey Kong's strength, to overcome various challenges and defeat the bad guy.
Mario is often a popular choice. Since both are Nintendo characters, it's easy to imagine crossovers. Mario's acrobatic skills and Donkey Kong's strength could create some really fun scenarios.
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.
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 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 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.
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.
Maybe a new original villain could be created for the fanfic. This villain could be a powerful mage who has the ability to manipulate time. He wants to use Cloud and Terra's powers for his own evil purposes. He tries to turn them against each other by showing them false visions of the future where they are enemies.
It could be a power - hungry ninja from within the Hidden Cloud Village who sees Raikage's relationship with Hinata as a threat to his own plans for taking over the village. He might try to spread false rumors about Hinata being a spy to turn the villagers against her and the Raikage.
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.