A rogue ninja from a neighboring village could be the villain. This ninja might have a vendetta against Ino's family and uses Naruto as a tool to get to her. He hypnotizes Naruto because he knows Naruto is strong and his actions while hypnotized would create a lot of trouble for Ino and Konoha.
One possible plot could be that an enemy uses a new jutsu to hypnotize Naruto and then makes him target Ino. Naruto, under the hypnosis, starts acting strangely towards Ino, which causes confusion among their friends. The story could then revolve around how their friends try to figure out what's wrong with Naruto and break the hypnosis before he does something really bad to Ino.
Maybe an evil wizard - like character from a far - off land. He hears about the pet in the Naruto universe and decides to capture it to use in his dark magic experiments. His arrival in the village causes chaos, and Naruto, Ino and the pet have to stop him from achieving his evil goals.
It could be Orochimaru. He might be interested in Ino's unique abilities, like her mind - control jutsu, for his own evil experiments. So he kidnaps her, and Naruto has to fight against Orochimaru's snake - like techniques to save Ino.
One possible plot could be that Naruto is hypnotized by an enemy ninja who wants to use him against the Hidden Leaf. Ino, being a skilled mind - user herself, tries to break the hypnosis. She has to first understand the nature of the hypnosis, which might be a complex jutsu. Then she dives into Naruto's mind, where she encounters various manifestations of Naruto's fears and desires. Ino has to navigate through these to reach the core of his mind and free him from the hypnosis.
Ino would likely be very concerned. She might immediately try to use her mind - reading skills to figure out what has happened to Naruto. If she can't break the hypnosis right away, she'd probably seek help from her teammates or sensei. Ino is a determined character, so she won't give up easily on saving Naruto.
Perhaps an evil organization that wants to capture Ino for her unique mind - related abilities. They believe they can use her powers for their own malicious purposes. Naruto and the rest of the team then have to protect Ino and take on this organization. The leader of this group could be the main villain, with his own set of powerful and dark jutsu.
A rogue ninja from another village who is jealous of Ino's talents and the reputation of her village could be the villain. This ninja might think that by kidnapping Ino, they can bring down the morale of her village and prove their own superiority.
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.
Orochimaru would make a great villain. He could be jealous of the new magical powers in the village and try to steal them for his own experiments. His snake-like abilities could be enhanced in a creepy way to contrast with the bright and shiny magical girl powers.
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.