Perhaps it could be an ancient god who has been awakened from a long slumber and wants to take over the world. This god would have powers that rival Wonder Woman's.
It could be a powerful sorceress. She might be jealous of Wonder Woman's popularity and power. So she uses her dark magic to create all kinds of problems for Wonder Woman, like casting spells on the people Wonder Woman loves or causing natural disasters.
There's a possibility that the main antagonist is a group of super - intelligent robots created by a mad scientist. They are programmed to destroy all forms of organic life. Wonder Woman has to find a way to stop them, which is difficult because they are constantly evolving and adapting to her attacks.
An ancient evil god could be the antagonist. This god has been awakened from a long slumber and sees Wonder Woman as a threat. He uses his dark magic to transform her into a giantess, thinking that her new form will make her an outcast among the people. He then tries to take over the world while Wonder Woman is struggling to adjust to her new size. But she overcomes the difficulties and uses her giant form to fight the god and save the world.
The Green Goblin could also fit well. He could form an alliance with some of Wonder Woman's foes. His chaotic nature and love for destruction would contrast with the heroes' quest for peace. He could target both of them, trying to break their partnership and cause mayhem in the city.
Lex Luthor could be a great main antagonist. He could be jealous of the trio's popularity and see them as a threat to his own power - hungry plans. He might create elaborate traps and use his vast resources and intellect to try and take them down, all while trying to make it look like they are the bad guys in the public eye.
Maybe it's an ancient evil entity that has been awakened by the combined power of Naruto's chakra and Wonder Woman's divine energy. This entity sees them as a threat to its plan of ruling both universes and thus tries to eliminate Wonder Woman first, which is when Naruto steps in to save her.
Lex Luthor could be a great antagonist. He could be jealous of the new alliance between Wonder Woman and Batman and see them as a threat to his own plans for world domination. He might use his intellect and resources to try and turn the public against them or create some high - tech weapons to take them on.
The Cheetah could be a good choice too. She could be working with some high - tech criminals to steal some powerful artifacts. Her speed and ferocity combined with the new allies she has made could put Batman and Wonder Woman in a tough spot as they try to stop her from achieving her evil goals.
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.
The Joker could also be a main antagonist in this fanfic. He could be interested in causing chaos not only in Gotham but also in the world of Wonder Woman. His unpredictable nature and love for mayhem would make him a formidable foe for the two heroes. He might come up with a plan that plays on their differences and tries to drive a wedge between them while also causing destruction.
There could be an ancient evil that is awakened by the birth of their son. This entity could see the son as a threat to its plans for world domination. It might have powers that are beyond what the son initially thinks he can handle, but through his own growth and the help of his parents' friends, he is able to overcome this powerful antagonist.
The Cheetah could also be a main antagonist. She could be working with some anti - hero or anti - superhuman group. She uses her speed and cunning to set up situations where Batman and Wonder Woman seem to be causing trouble. For example, she could steal something and make it look like they did it.