A new character could be introduced as the main antagonist. This character could be from a far - off land where Titan shifting has been practiced in a more evil way. He comes to the Naruto world to spread chaos and destruction, believing that the power of the Titans should dominate all. Naruto has to learn about this new enemy's ways and use his own unique Titan - shifting abilities, along with his ninja skills, to defeat him.
It could be Orochimaru. He's always been interested in power and forbidden jutsu. In this fanfic, he might discover the power of Titan shifting and try to use it for his own gain. He could experiment on people to create more Titan shifters under his control, and Naruto would have to stop him from creating an army of these powerful beings.
A powerful rogue ninja who has mastered a forbidden jutsu that gives him the ability to control minds could be a great main antagonist. He could use this power to turn Naruto's friends against him, creating a lot of internal conflict within the group.
A power - hungry warlord could be a great main antagonist. He might see the Queens Titan as a threat to his plans of total domination and constantly try to undermine or destroy it. He could have a large army and advanced weaponry at his disposal.
The Kingpin might be a good choice. He could see the Titans as a new weapon to use in his criminal empire. He could form an alliance with some of the more corrupt elements in the Attack on Titan world, like some of the military commanders who are only interested in power. He would use his wealth and influence to control the Titans and try to take over both universes. Spider - Man and the heroes from Attack on Titan would have to fight against his well - organized and well - funded forces.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
A new character could be created as the antagonist. For example, an Uchiha who has been corrupted by the power of the Sharingan and wants to use Naruto's special Uchiha - related abilities for his own evil purposes. This character could be jealous of Naruto's unique position within the Uchiha - related story and try to take it from him.