Perhaps an ancient evil force that has been awakened and targets Naruto's son because of his special chakra. The force might want to use the son's power for its own dark purposes.
There's also the possibility that a group of disgruntled villagers, who are jealous of Naruto's position, plot to kidnap his son to undermine Naruto's status. They could be the main antagonists in the fanfiction.
It could be a rogue ninja who has a vendetta against Naruto. This ninja might see Naruto's son as a way to get back at Naruto for past defeats or slights.
It could be someone who wants to use Naruto's connection to the scar for their own evil purposes. Maybe a rogue ninja who believes that the scar holds some kind of dark power that can be harnessed.
Perhaps an old enemy from Naruto's past that was thought to be defeated has resurfaced. This enemy might have targeted Naruto's wife as a way to get revenge on Naruto for their previous defeats. They could be using her as a bait to lure Naruto into a trap.
It could be someone who wants to use Naruto's unique heritage against him. Maybe a villain from the Naruto universe who sees Naruto's connection to Harley Quinn as a weakness. For example, Orochimaru might want to capture Naruto to study his strange combination of powers.
It could be Orochimaru. He's always after power and seeing Naruto with Son Goku's power would make him a prime target. He might try to extract the power from Naruto for his own evil experiments.
A possible main antagonist in such a fanfic could be a dark entity that has possessed someone close to Naruto. This entity could be using the host's body to get close to Naruto and then attacks him, resulting in the loss of his arm. Naruto would then have to figure out not only how to deal with his injury but also how to save his friend from the dark entity'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.
It could be a Decepticon who sees the 'Son of the Stars' as a threat to their plans for domination. Maybe a powerful Decepticon leader who fears the special powers that the 'Son of the Stars' might possess.
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.