Danzo could be a great antagonist. He was always a bit of a shadowy figure in the Naruto series. In this 'Only Male Alive' fanfiction, he might emerge as a dictator - like figure. He could be trying to enforce his strict, often controversial rules on the remaining male ninjas, seeing Naruto as a threat to his new - found power and control.
Madara Uchiha could also be the main antagonist. Maybe in this altered world, his plan for eternal peace through the Infinite Tsukuyomi takes on a new form. With only males alive, he could be manipulating them to further his own ends, believing that only through his extreme vision can the male - only ninja world survive and thrive, and Naruto has to stop him.
The main antagonists could be a group of rogue male ninjas who oppose Naruto's vision of rebuilding the ninja world. They might believe in a more ruthless and power - hungry approach, seeing the situation as an opportunity to take over. Another possibility is that an ancient evil, sealed away long ago, is released due to the imbalance in the ninja world with only male ninjas alive. This evil entity could be extremely powerful and have motives related to destroying the new order that Naruto is trying to establish.
Well, in this 'Naruto Only Male Alive' fanfiction, perhaps Naruto wakes up one day to find only male ninjas around. He then decides to create a new ninja order. He starts by training the younger male ninjas more rigorously, teaching them not just combat skills but also the importance of unity. As he does this, he uncovers secrets about a prophecy that only a male ninja can fulfill in this strange new world, and he has to rise to the occasion.
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.
It could be a new dark wizard who is envious of Harry's speed. This wizard might want to steal Harry's power for himself and use it to take over the wizarding world.
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.
It could be a rogue ninja who wants to disrupt Naruto's business to gain power. Maybe he's jealous of Naruto's success and popularity in the business world. He could try to steal Naruto's business secrets or sabotage his operations.
It could be a rogue Kumo ninja who is jealous of Naruto's power and wants to prove himself by defeating Naruto. This ninja might have some dark secrets and a grudge against Kumo as well.
It could be Orochimaru. He's always been interested in immortality and reanimation techniques. Maybe he reanimates Naruto for some evil purpose, like using Naruto's power to take over the ninja world.