Maybe it could be an evil wizard named Zoltar. He has been observing both universes for a long time and has found a way to combine the powers of the tailed beasts and the Dragon Balls for his own evil purposes. He uses this power to create powerful minions that Naruto and Goku have to fight through before they can face him directly.
A powerful demon named Malice could be the main villain. He has the ability to absorb both chakra and ki, making him a formidable foe for Naruto and Goku. He has a dark plan to destroy both the Naruto universe and the Dragonball Super universe and create his own realm of chaos.
An ancient being called the Void Lord could be the main villain. This entity exists outside of both universes and is jealous of the life and energy within them. It sends its avatars into the Naruto and Dragonball Super universes to cause destruction and steal powers. Naruto and Goku must figure out how to reach the Void Lord in its own dimension and stop it before it completely destroys everything they hold dear.
In this 'naruto and dargonball super fanfic' plot, the universes of Naruto and Dragonball start to merge. Naruto and his friends find themselves in a strange new world filled with Saiyans and other Dragonball characters. Goku discovers that Naruto has a unique form of energy similar to ki. They decide to train together to become stronger. Along the way, they face challenges like an ancient evil that has been awakened due to the universe merge and must use their combined skills and the help of their friends from both universes to defeat it.
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.
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.
A new character could be introduced as the main villain. This character could be someone from an ancient clan that was once in control of the 10 - tailed beast but lost it. Now, seeing Naruto with that power, they want it back and will stop at nothing to get it. They could have unique powers and abilities that make them a formidable foe for Naruto and his friends.
It could be a new character, a powerful dark wizard who wants to use the combined power of Naruto's chakra and Pikachu's electricity for his own evil purposes. He creates all sorts of dark creatures and sends them after Naruto and Pikachu to try and capture them. He's very cunning and has a lot of minions to do his bidding.
It could be a new character created specifically for this fanfic. Maybe someone who wants to steal Naruto's six - tailed power for themselves.
Another option could be a powerful shinobi from a forgotten clan that was once known for its wind - based abilities. This shinobi wants to revive his clan's former glory by any means necessary, even if it means going against Naruto and his friends. He could be using ancient wind - based techniques that no one has seen before, making him a formidable foe.
A powerful and mysterious organization could be the main villain. They have been secretly manipulating events in the ninja world for years, and now they plan to use a powerful weapon to destroy all the hidden villages and take over the world. Naruto has to expose and stop them.
A great option could be Orochimaru fused with Hades. Orochimaru's thirst for power and immortality combined with Hades' control over the Underworld would make a terrifying villain. He could be plotting to take over both the ninja world and the realm of Greek gods. He might use his dark jutsu and Hades' power over death to create an army of undead ninjas and mythological creatures.