Another option is that the villain is actually a group rather than an individual. A cult that worships an ancient and evil entity. They believe that by sacrificing the 'Son of the Stars', they can bring about the return of their dark god. They work in the shadows, manipulating events and people to achieve their goal.
A new character could be introduced as the main villain. This could be a powerful wizard or sorcerer who has a vendetta against the protagonist's family or race. They might be jealous of the powers that the 'Son of the Stars' possesses and want to take them for themselves. They could start by causing chaos in the protagonist's home town, slowly building up their power and influence.
It could be a rogue ninja who has a vendetta against Naruto and decides to target his son. Maybe this villain was once defeated by Naruto and now wants to take revenge by harming his family.
There is a possibility that an ancient and powerful dark creature could be the main villain. This creature, long forgotten in the wizarding world, resurfaces and targets Harry's son. It might believe that the boy has some special power or is the key to something it desires. As a result, it lures the son away and hides him in a remote and dangerous place. Harry has to figure out what this creature is and how to defeat it to get his son back.
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.
A rogue ninja who has made a pact with dark forces. He wants to use Goku's son to open a portal to the Saiyan planet and then invade it. He would be constantly trying to manipulate the situation to get Goku's son to do his bidding. He has a team of minions who are also skilled in both ninjutsu and some dark form of ki - like powers.
Maybe an ancient evil spirit that has been awakened due to some mistake. It targets Ageha because she has a pure and powerful chakra. Naruto, being the hero he is, tries to fight the spirit, but he quickly realizes that he needs Ageha's help as well as the help of all his friends to defeat this powerful foe.
Perhaps an ancient evil spirit that has been awakened by the mixing of the two worlds - Ariel's underwater world and Mowgli's jungle world. This spirit wants to plunge both worlds into darkness. It starts by causing natural disasters in both areas, like huge storms in the ocean and forest fires in the jungle. Ariel and Mowgli must figure out a way to stop this spirit before it's too late, by finding ancient artifacts that can seal the spirit away again.
There could be a group of rogue Huntsmen who believe that the current system of protecting the world is flawed. They form a radical organization and start causing chaos. Their leader, who is a very powerful and charismatic character, could be the main villain. They would have their own set of ideals and be willing to do whatever it takes to achieve their goals, even if it means going against the established order.
A jealous ex - employee of Game Shakers could be a great villain. They were fired for some reason, like being caught stealing ideas, and now they want revenge. They could try to sabotage the company's new projects and spread false rumors about the Game Shakers.
The main villain could be Darkseid. Imagine if he somehow finds a way to enter the Naruto universe. He would be a formidable foe for both Naruto and Supergirl. His omega beams and immense strength would be a huge challenge for them to overcome.
It could be a rogue ninja from the village with the Tenshikage. Maybe he's jealous of the Tenshikage's power and wants to take it for himself. He could be causing chaos in the village, stealing important ninja scrolls and attacking innocent villagers.