It could be a rogue ninja who created the zombie plague on purpose. Maybe they wanted to take over Konoha or the whole ninja world by using the zombies as an army.
Perhaps it's an ancient evil spirit that was awakened and it has the power to reanimate the dead. This spirit could be really powerful and Naruto has to figure out its weaknesses to defeat it. It would be constantly summoning more zombies to wear Naruto down.
Maybe an ancient evil ninja who was sealed away long ago but has now been released. This antagonist could have powers that nullify any communication or summoning jutsu, forcing Naruto to fight alone. He would be extremely powerful and know many forgotten and deadly jutsu.
The main antagonist could be Agamemnon. In the original story, he and Achilles had a lot of conflict. In this fanfiction, if Achilles is fighting for Troy, Agamemnon would still be leading the Greek forces against him. His thirst for power and glory would make him a formidable foe, constantly devising strategies to defeat Achilles and take Troy.
It could be a new dark wizard who is more powerful and cunning than Voldemort. This wizard might have been in hiding all this time, biding his time to take over the wizarding world. With Harry being alone, he would pose a great threat as Harry doesn't have his friends to support him in this fight.
Maybe an evil Namekian. Namekians have unique powers, and an evil one could use his abilities to manipulate the life energy in a way that creates zombies. He might be jealous of the Saiyans' power and wants to use the zombies to wipe them out. He could also be in cahoots with some of the other villains from the Dragon Ball series, like Cell. The heroes would have to not only fight the zombies but also figure out this Namekian's motives and how to stop him.
Well, the plot could involve Naruto being in a post - apocalyptic world filled with zombies. His ninja skills would be put to the extreme test. He could team up with his friends like Sasuke and Sakura. Naruto would have to adapt his fighting style as zombies don't feel pain like normal foes. He might use his speed and agility to dodge the zombies and then use his powerful ninjutsu to take them out in groups.
It could be a dark wizard who also wants to control the zombies but for evil purposes. Maybe a long - lost relative of Voldemort who has emerged from the shadows and sees the zombies as a means to finally take over the wizarding world. He might try to steal Harry's method of controlling them or create more powerful zombies that are immune to Harry's control.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.
Krampus himself could be the main antagonist. Since he is a figure known for punishing the naughty, his actions in the Naruto world might be seen as unjust. He could be going after ninjas without really understanding their motives, causing a lot of trouble for the main characters.
It could be a rogue ninja who also has somehow acquired bankai - like powers. This antagonist might be jealous of Naruto's newfound abilities and wants to prove that he is the stronger one. So he starts causing chaos in the ninja world, challenging Naruto at every turn.