Maybe a new character created specifically for this fanfic. A powerful sorcerer who wants to use Naruto's chakra and Slade's combat expertise for his own evil purposes. He could be manipulating events from the shadows, pitting Naruto and Slade against each other at first until they realize they are being played.
The main antagonist could be Madara. Even though Obito was once following Madara's plan, with Naruto joining Obito, Madara might see this as a threat to his grand scheme. He could try to manipulate events to drive a wedge between Naruto and Obito or directly attack them to stop their new alliance from achieving their goals.
It could be Thanos. Since he is a powerful and menacing force in Loki's universe. He might see Harry as an unexpected variable and want to eliminate him. Also, his goal of collecting the Infinity Stones could put him at odds with both Harry and Loki as they might try to stop him to protect their respective worlds.
Well, one possibility could be that Naruto, with his ninja skills and strong sense of justice, joins Slade for a common goal like fighting a greater evil that neither could face alone. Maybe they team up to take on a powerful, shadowy organization that threatens both their worlds.
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.
Perhaps an old enemy of one of the members of Team 9 shows up. Since Naruto has joined the team, they might see it as an opportunity to get revenge. This antagonist could be someone who was once defeated by the member's family and now wants to prove themselves. They would be very cunning and use their knowledge of the team member's past to try and divide the team.
It could be an old enemy who has resurfaced, like Orochimaru again. Since Naruto and Sasuke are together now, Orochimaru might see them as a threat to his own plans for power and immortality.
It could be an old enemy of the Hunters. Maybe a powerful monster that has a grudge against them for past defeats. For instance, a giant who has been waiting for the right time to strike back at the Hunters.
It could be a rogue wizard who has infiltrated SHIELD and is using their technology for dark magic purposes. This wizard might be jealous of Harry's new position and try to undermine him.
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 Orochimaru. He might be interested in Baby Beel's powers and try to capture him for his own evil experiments. Orochimaru would see Beel as a unique specimen and would stop at nothing to get his hands on him. Naruto would then have to use all his skills and the bond he has with Beel to keep him safe from Orochimaru.