A cyborg assassin could be a new villain. This villain could have been created by a shadowy organization to take out Spiderman 2099. With enhanced strength, speed, and the ability to hack into any digital system in the city.
There could be a genetic experiment gone wrong. A scientist trying to create a super - soldier for the future military ends up creating a monstrous being with spider - like abilities but a twisted mind. This villain would be constantly challenging Spiderman 2099 in both physical combat and mental games.
There could be a genetic engineer gone bad. This villain creates dangerous hybrid creatures and releases them in the city, forcing Spider - Man 2099 to fight these unpredictable beasts. He might also have to figure out how to reverse the genetic mutations.
Perhaps an ancient evil spirit that was awakened due to some of the events related to Naruto's regeneration. This spirit could have its own motives, like corrupting the ninja world and turning it into a place of chaos and destruction.
Some of the big names in the comic industry could be behind it. For example, Stan Lee, if he were still alive, would have been a great candidate. But nowadays, it could be someone like Mark Millar who is known for his innovative storytelling. There are also many great artists who might be part of it, like Alex Ross who is famous for his detailed and realistic art.
There are several potential villains. In the Naruto world, Orochimaru would surely be interested in Naruto's new Ultraman powers. He might try to experiment on Naruto to figure out how to obtain those powers for himself. From the Ultraman world, the Alien Mefilas could be a villain. They are known for their cunning and would likely see Naruto as a target. Additionally, some of the rogue ninja in the Naruto world who are power - hungry might team up with the Ultraman villains. They could form an alliance to take over both worlds, seeing Naruto's unique powers as the key to their success.
The Vulture could be a new and more menacing villain. Maybe he's using the post - Civil War chaos to his advantage, stealing high - tech equipment that was left unguarded during the Avenger's split. He could be targeting Spider - Man specifically, seeing him as an easy target now that he doesn't have the full support of the Avengers.
A possible villain could be a rogue demigod who has somehow made his way into Jonas's world. This demigod, let's call him Damian, is jealous of Percy's status and wants to create chaos in both worlds. He uses the strict order of Jonas's community to his advantage, turning the Elders against any outsiders like Percy, and also tries to steal Percy's powers by using some dark magic he learned from an ancient scroll.
One potential villain could be a rogue Death Eater who escaped justice. This Death Eater might see Teddy as a symbol of the new generation that he wants to destroy. Another could be a jealous wizard who is envious of Teddy's special abilities, like his Metamorphmagus powers, and tries to harm him. Harry would then have to fight these villains to protect Teddy.
There could be an ancient evil entity that has been awakened. This entity has the power to corrupt minds and cause destruction on a large scale. It targets the Avengers because they are the most powerful force on Earth that can oppose it. Daisy Johnson has to use her powers not only to fight the entity physically but also to resist its mind - corrupting influence, while the rest of the Avengers try to find a way to banish the entity back to its slumber.
A really good villain could be an ancient Titan who has been awakened from his slumber. He's angry at the gods and wants to take revenge by destroying their favorite demigods, Percy and Annabeth. He has the power to manipulate earth and fire, which makes him a formidable foe.
Dr. Eggman could still be a major villain. He might see Sonic's new vampire state as an opportunity to study and use it for his own evil plans. Maybe he tries to create an army of vampire robots. Another potential villain could be an ancient vampire lord who sees Sonic as a threat to his rule over the vampire world.