It could be Voldemort who somehow manages to cross over into the Star Wars universe. He might see the power of the Force as something to be harnessed for his own evil purposes. His dark magic would be a great contrast to the light - side teachings of Yoda, and Harry and Yoda would have to team up to stop him.
Maybe a Sith Lord from the Star Wars universe decides to target Harry because he senses the great power within him. This Sith Lord could be the main antagonist. He would try to turn Harry to the dark side, but with Yoda's guidance, Harry would resist. The conflict between the Sith Lord's evil plans and Harry and Yoda's attempts to protect the balance would be the central conflict of the fanfic.
It could be a new Sith Lord. This Sith Lord could be someone who has been in hiding for a long time, gathering power and knowledge. They see Ashoka and Yoda's reunion as a threat to their plans of taking over the galaxy. So, they start to target them and try to disrupt their new - found bond.
In a 'harry meets master yoda fanfic', it could start with Harry having a strange dream about a small, green, wise - looking creature. Later, he actually meets Master Yoda. Yoda is intrigued by Harry's unique brand of magic. They could engage in philosophical discussions about power, responsibility, and destiny. Harry could learn from Yoda's wisdom and use it to face the upcoming threats in his own wizarding world when he returns.
The main antagonist might be a being from another dimension who is able to manipulate both magic and the Hulk's gamma - irradiated energy. This being wants to use the chaos caused by the meeting of Harry and the Hulk to open a portal to let in more of his kind to take over all the universes. He sets traps for Harry and the Hulk and constantly tries to keep them from working together to stop him.
Perhaps a rogue Overwatch agent who has turned against the organization. When Harry arrives, this agent sees an opportunity. He believes that by using Harry's magic, he can take over Overwatch and rule the world. So he tries to manipulate Harry and turn him against Tracer and the rest of the good - hearted Overwatch members.
It could be a power - hungry alien leader who wants to take over Hogwarts and use its magic for their own empire.
A dark wizard from the Harry Potter universe could be the main antagonist. Maybe a follower of Voldemort who escaped the final battle and found his way to Byakko's world. He sees the power of Byakko and wants to use it for his own evil purposes. He could try to enslave Byakko and use its power to take over both the wizarding world and Byakko's realm.
Most likely, Medusa would be the main antagonist. Her ability to turn people to stone makes her a very dangerous foe for Harry Potter and the other characters in the wizarding world.
It could be a dark fairy who wants to use the power of both the wizarding world and Pixie Hollow for her own evil purposes. She might try to steal the magic from Hogwarts and the pixie dust from Pixie Hollow to become all - powerful.
Maybe the main antagonist could be Ra's al Ghul. He's always interested in power, and if he got his hands on some magic from the Harry Potter universe, he could become an even greater threat. He could try to use the magic to bring about his vision of a 'perfect' world, which would be at odds with both Harry's and Nightwing's ideas of justice. So they'd have to join forces to stop him from achieving his goals.
A new alien species could be the main antagonist. This species could have technology that is completely unknown to both Noble Six and Master Chief. They would have to quickly learn about the new enemy's weaknesses while also trying to survive their initial attacks. This would test their adaptability and teamwork skills.